3422 lines (3421 with data), 241.8 kB
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"from __future__ import print_function\n",
"import pandas as pd \n",
"import matplotlib.pyplot as plt \n",
"import numpy as np \n",
"from scipy.stats import zscore\n",
"import seaborn as sns\n",
"import sys,os\n",
"from mapper import expand, parse_mapping_table, apply_mappers\n",
"%matplotlib inline"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"gene_id = \"ENTREZID\"\n",
"raw_data_dir = \"/home/olya/SFU/Hossein/PDX/\" \n",
"preprocessed_data_dir = \"/home/olya/SFU/Hossein/v2/preprocessed/exprs/\"\n",
"root_dir = \"/home/olya/SFU/Hossein/v2/\"\n",
"# wget https://media.nature.com/original/nature-assets/nm/journal/v21/n11/extref/nm.3954-S2.xlsx\n",
"# download Entrez ID mapping file"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# PDX \n",
"\n",
"- for 22665 Gene symbols are converted to Gene IDs \n",
"- gene expression profiles (FPKM) for 399 samples converted to log2(TPM+1)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"(22665, 399)\n"
]
},
{
"data": {
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"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>X-1004</th>\n",
" <th>X-1008</th>\n",
" <th>X-1027</th>\n",
" <th>X-1095</th>\n",
" <th>X-1119</th>\n",
" <th>X-1156</th>\n",
" <th>X-1167</th>\n",
" <th>X-1169</th>\n",
" <th>X-1172</th>\n",
" <th>X-1173</th>\n",
" <th>...</th>\n",
" <th>X-5713</th>\n",
" <th>X-5717</th>\n",
" <th>X-5727</th>\n",
" <th>X-5739</th>\n",
" <th>X-5808</th>\n",
" <th>X-5959</th>\n",
" <th>X-5974</th>\n",
" <th>X-5975</th>\n",
" <th>X-6030</th>\n",
" <th>X-6047</th>\n",
" </tr>\n",
" <tr>\n",
" <th>Sample</th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
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" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>A1BG</th>\n",
" <td>2.75</td>\n",
" <td>8.97</td>\n",
" <td>0.14</td>\n",
" <td>0.13</td>\n",
" <td>0.08</td>\n",
" <td>17.52</td>\n",
" <td>0.18</td>\n",
" <td>0.41</td>\n",
" <td>0.08</td>\n",
" <td>0.00</td>\n",
" <td>...</td>\n",
" <td>21.24</td>\n",
" <td>0.46</td>\n",
" <td>18.70</td>\n",
" <td>0.00</td>\n",
" <td>8.30</td>\n",
" <td>14.41</td>\n",
" <td>5.09</td>\n",
" <td>6.35</td>\n",
" <td>0.09</td>\n",
" <td>3.22</td>\n",
" </tr>\n",
" <tr>\n",
" <th>A1BG-AS1</th>\n",
" <td>2.48</td>\n",
" <td>3.25</td>\n",
" <td>0.00</td>\n",
" <td>0.00</td>\n",
" <td>0.00</td>\n",
" <td>6.52</td>\n",
" <td>0.00</td>\n",
" <td>0.00</td>\n",
" <td>0.00</td>\n",
" <td>0.00</td>\n",
" <td>...</td>\n",
" <td>15.21</td>\n",
" <td>0.09</td>\n",
" <td>3.42</td>\n",
" <td>0.00</td>\n",
" <td>8.30</td>\n",
" <td>8.36</td>\n",
" <td>3.71</td>\n",
" <td>4.52</td>\n",
" <td>0.00</td>\n",
" <td>3.24</td>\n",
" </tr>\n",
" <tr>\n",
" <th>A1CF</th>\n",
" <td>0.02</td>\n",
" <td>0.03</td>\n",
" <td>1.30</td>\n",
" <td>2.83</td>\n",
" <td>2.87</td>\n",
" <td>0.72</td>\n",
" <td>3.41</td>\n",
" <td>0.01</td>\n",
" <td>1.84</td>\n",
" <td>2.96</td>\n",
" <td>...</td>\n",
" <td>0.01</td>\n",
" <td>0.45</td>\n",
" <td>0.00</td>\n",
" <td>0.01</td>\n",
" <td>0.00</td>\n",
" <td>0.00</td>\n",
" <td>0.02</td>\n",
" <td>0.03</td>\n",
" <td>4.63</td>\n",
" <td>0.02</td>\n",
" </tr>\n",
" <tr>\n",
" <th>A2LD1</th>\n",
" <td>4.87</td>\n",
" <td>0.81</td>\n",
" <td>6.45</td>\n",
" <td>4.94</td>\n",
" <td>11.07</td>\n",
" <td>0.87</td>\n",
" <td>3.28</td>\n",
" <td>0.32</td>\n",
" <td>0.61</td>\n",
" <td>7.10</td>\n",
" <td>...</td>\n",
" <td>1.33</td>\n",
" <td>2.51</td>\n",
" <td>2.67</td>\n",
" <td>3.13</td>\n",
" <td>0.44</td>\n",
" <td>2.96</td>\n",
" <td>0.00</td>\n",
" <td>1.99</td>\n",
" <td>2.57</td>\n",
" <td>1.50</td>\n",
" </tr>\n",
" <tr>\n",
" <th>A2M</th>\n",
" <td>0.01</td>\n",
" <td>71.17</td>\n",
" <td>0.00</td>\n",
" <td>3.69</td>\n",
" <td>0.00</td>\n",
" <td>58.16</td>\n",
" <td>0.00</td>\n",
" <td>0.02</td>\n",
" <td>94.12</td>\n",
" <td>0.02</td>\n",
" <td>...</td>\n",
" <td>463.32</td>\n",
" <td>0.04</td>\n",
" <td>33.35</td>\n",
" <td>0.00</td>\n",
" <td>254.97</td>\n",
" <td>41.52</td>\n",
" <td>2.32</td>\n",
" <td>0.00</td>\n",
" <td>0.00</td>\n",
" <td>0.16</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>5 rows × 399 columns</p>\n",
"</div>"
],
"text/plain": [
" X-1004 X-1008 X-1027 X-1095 X-1119 X-1156 X-1167 X-1169 \\\n",
"Sample \n",
"A1BG 2.75 8.97 0.14 0.13 0.08 17.52 0.18 0.41 \n",
"A1BG-AS1 2.48 3.25 0.00 0.00 0.00 6.52 0.00 0.00 \n",
"A1CF 0.02 0.03 1.30 2.83 2.87 0.72 3.41 0.01 \n",
"A2LD1 4.87 0.81 6.45 4.94 11.07 0.87 3.28 0.32 \n",
"A2M 0.01 71.17 0.00 3.69 0.00 58.16 0.00 0.02 \n",
"\n",
" X-1172 X-1173 ... X-5713 X-5717 X-5727 X-5739 X-5808 \\\n",
"Sample ... \n",
"A1BG 0.08 0.00 ... 21.24 0.46 18.70 0.00 8.30 \n",
"A1BG-AS1 0.00 0.00 ... 15.21 0.09 3.42 0.00 8.30 \n",
"A1CF 1.84 2.96 ... 0.01 0.45 0.00 0.01 0.00 \n",
"A2LD1 0.61 7.10 ... 1.33 2.51 2.67 3.13 0.44 \n",
"A2M 94.12 0.02 ... 463.32 0.04 33.35 0.00 254.97 \n",
"\n",
" X-5959 X-5974 X-5975 X-6030 X-6047 \n",
"Sample \n",
"A1BG 14.41 5.09 6.35 0.09 3.22 \n",
"A1BG-AS1 8.36 3.71 4.52 0.00 3.24 \n",
"A1CF 0.00 0.02 0.03 4.63 0.02 \n",
"A2LD1 2.96 0.00 1.99 2.57 1.50 \n",
"A2M 41.52 2.32 0.00 0.00 0.16 \n",
"\n",
"[5 rows x 399 columns]"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"exprs = pd.read_excel(raw_data_dir+\"nm.3954-S2.xlsx\",\"RNAseq_fpkm\")\n",
"exprs.set_index(\"Sample\",inplace=True,drop=True)\n",
"print(exprs.shape)\n",
"exprs.head() "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Mapping of gene symbols to EntrezID using current gene_info file prowided by NCBI:\n",
"\n",
"\n",
" * Download the unzip the file \n",
"\\# wget ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz\n",
"\\# gunzip Homo_sapiens.gene_info.gz;\n",
" * Specify *hgnc_file* variable in this notebook\n",
" * Mapping strategy\n",
" \n",
"1). Unknown genes and genes belonging to organisms other than H.sapiens were excluded.\n",
"\n",
"2). First each query symbol was tried to match with any of current \"Symbol\" directly. If the query symbol mapped to one of current symbol but has no Gene ID, the query symbol was marked as not mapped. \n",
"\n",
"3). If the query symbol matches none of current symbols, we tried to match it with one of \"Synonyms\". Genes matched no synonym as well as matched ambiguous synonyms correponding more than one Gene ID were condiered not mapped. \n",
"\n",
"4). At this point, many of not recognized symbols had LOCXXXXXXXXX format. \n",
"According to the documntation provided by NCBI: \"Symbols beginning with LOC. When a published symbol is not available, and orthologs have not yet been determined, Gene will provide a symbol that is constructed as 'LOC' + the GeneID. This is not retained when a replacement symbol has been identified, although queries by the LOC term are still supported. In other words, a record with the symbol LOC12345 is equivalent to GeneID = 12345. So if the symbol changes, the record can still be retrieved on the web using LOC12345 as a query, or from any file using GeneID = 12345\" e.g. :\n",
"\n",
" - LOC100093631 -> 100093631 \n",
" - LOC100129726 -> 100129726\n",
" - etc. \n",
"\n",
"Therefore all genes started with LOC were converted to Gene IDs removing \"LOC\" from query term. If resulting Gene ID matched none of current Gene IDs the symbol was considered not mapped. \n",
"\n",
"4). Several pairs of query gene symbols matched current symbol and synonym of the same Entrez gene ID, e.g. AGAP8 and AGAP4, ANXA8L1 and ANXA8L2, etc.\n",
"Expressions of these genes were summarized because such genes were merged to a single gene in newer assembly versions."
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"2547 rows with both Previous Symbols and Entrez Gene ID empty\n",
"Ok: no duplicated pairs detected\n",
"27336 rows with empty Previous Symbols were excluded\n",
"173 Previous Symbols ids mapped to no Entrez Gene ID\n",
"83 Previous Symbols mapped to multiple Entrez Gene ID\n",
"4697 different Previous Symbols mapped to the same Entrez Gene ID\n",
"9336 Previous Symbols can be mapped directly to Entrez Gene ID\n"
]
}
],
"source": [
"hgnc_file = root_dir+\"HGNC_5.10.2018.txt\"\n",
"\n",
"hgnc = pd.read_csv(hgnc_file, sep =\"\\t\",index_col=0)#\n",
"#print(hgnc.shape, len(set(hgnc.index.values)))\n",
"approved = hgnc.loc[hgnc[\"Status\"] == \"Approved\",:]\n",
"hgnc_prev = expand(approved[[\"Previous Symbols\",\"Entrez Gene ID\"]],column=\"Previous Symbols\",sep=\", \") \n",
"hgnc_prev = parse_mapping_table(hgnc_prev, \"Previous Symbols\",\"Entrez Gene ID\")"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"2224 rows with both Synonyms and Entrez Gene ID empty\n",
"Ok: no duplicated pairs detected\n",
"18283 rows with empty Synonyms were excluded\n",
"662 Synonyms ids mapped to no Entrez Gene ID\n",
"962 Synonyms mapped to multiple Entrez Gene ID\n",
"27509 different Synonyms mapped to the same Entrez Gene ID\n",
"10612 Synonyms can be mapped directly to Entrez Gene ID\n"
]
}
],
"source": [
"hgnc_syn = expand(approved[[\"Synonyms\",\"Entrez Gene ID\"]],column=\"Synonyms\",sep=\", \") \n",
"hgnc_syn = parse_mapping_table(hgnc_syn, \"Synonyms\",\"Entrez Gene ID\")"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Ok: no empty rows detected\n",
"Ok: no duplicated pairs detected\n",
"Ok: All Symbol rows are not empty.\n",
"Ok: All Symbol are mapped to GeneID\n",
"16 Symbol mapped to multiple GeneID\n",
"Ok: All GeneID are unique\n",
"59266 Symbol can be mapped directly to GeneID\n"
]
}
],
"source": [
"NCBI = pd.read_csv(root_dir+\"Homo_sapiens.gene_info\",sep = \"\\t\")\n",
"NCBI = NCBI[[\"#tax_id\",\"GeneID\",\"Symbol\",\"Synonyms\",\"type_of_gene\"]]\n",
"NCBI = NCBI.loc[NCBI[\"#tax_id\"] == 9606]\n",
"NCBI = NCBI.loc[NCBI[\"type_of_gene\"] != \"unknown\"]\n",
"ncbi_symbols = parse_mapping_table(NCBI, \"Symbol\",\"GeneID\")"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Ok: no empty rows detected\n",
"Ok: no duplicated pairs detected\n",
"Ok: All Synonyms rows are not empty.\n",
"Ok: All Synonyms are mapped to GeneID\n",
"3145 Synonyms mapped to multiple GeneID\n",
"49179 different Synonyms mapped to the same GeneID\n",
"10839 Synonyms can be mapped directly to GeneID\n"
]
}
],
"source": [
"ncbi_synonyms = expand(NCBI[[\"Synonyms\",\"GeneID\"]],column=\"Synonyms\",sep=\"|\") \n",
"ncbi_synonyms = parse_mapping_table(ncbi_synonyms, \"Synonyms\",\"GeneID\")"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Mapped: 22467 \n",
"\tdirectly via main_mapper 20272 \n",
"\tvia alternative mapper 471 \n",
"\tvia one of multiple synonyms in alternative mapper 1026 \n",
"\tLOC 698 \n",
"Unmapped: 198 \n",
"\trecognized symbols without Entrez ID 0 \n",
"\tmultiple query_ids map to the same target_id 0 \n",
"\tquery_ids map to multiple target_ids in the main mapper 0 \n",
"\tquery_ids map to multiple target_ids in the alternative mapper 54 \n",
"\tLOC not found in Entrez 26 \n",
"\tNot found at all: 118\n",
"Warning: query IDs mapping to duplicated target IDs in mapping table: 47\n",
"Warning: query IDs not mapped to any target IDs excluded: 198\n"
]
},
{
"ename": "AttributeError",
"evalue": "'tuple' object has no attribute 'head'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-9-c037e6e14d06>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0mexprs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mapply_mappers\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mexprs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mncbi_symbols\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mncbi_synonyms\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mverbose\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mTrue\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mhandle_duplicates\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"sum\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mexprs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mhead\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m5\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;31mAttributeError\u001b[0m: 'tuple' object has no attribute 'head'"
]
}
],
"source": [
"exprs = apply_mappers(exprs, ncbi_symbols, ncbi_synonyms, verbose = True,handle_duplicates = \"sum\")\n",
"exprs.head(5)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### FPKM to TPM conversion\n",
"Let $X_i$ is a number of fragments mapped to a transcript, $N$ is a total number of fragments sequensed (and assigned to any transcript) and $\\widetilde{l_i}$ is an effective length of a transcript (i.e. how many fragments with average length $\\mu_{frag}$ can generate a transcript of length $l_i$: $\\widetilde{l_i} = l_i - \\mu_{frag}+1$)\n",
"\n",
"*FPKM* - fragments per kilobase of exon (i.e. effective length) per million reads mapped\n",
"\n",
"$FPKM_i = \\frac{X_i}{\\frac{$\\widetilde{l_i}}{10^3}*\\frac{N}{10^6}} = \\frac{X_i}{l_iN}*10^9 $\n",
"\n",
"*TPM* - transcripts per million of transcripts.\n",
"\n",
"In turn, $\\frac{X_i}{\\widetilde{l_i}}$ is estimated number of transcripts \n",
"\n",
"$TPM_i = \\frac{\\frac{X_i}{\\widetilde{l_i}}}{\\sum_j{\\frac{X_j}{\\widetilde{l_j}}}}*10^6 $\n",
"\n",
"\n",
"### how to convert FPKM to TPM\n",
"Divide both numerator and denominator by $N$ and mutiply by $10^9$:\n",
"\n",
"$TPM_i = \\frac{\\frac{X_i}{N\\widetilde{l_i}}*10^9}{\\sum_j{\\frac{X_j}{N\\widetilde{l_j}}*10^9}}*10^6 = \\frac{FPKM_i}{\\sum_j{FPKM_j}} * 10^6$\n",
"\n",
"Sources:\n",
" - What the FPKM? https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/\n",
" - https://www.biostars.org/p/160989/\n",
" - Lior Pachter https://arxiv.org/pdf/1104.3889.pdf\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"## FPKM convert to log2(TPM+1)\n",
"sum_fpkm = exprs.apply(sum,axis=0)\n",
"sum_fpkm.head()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"tpm = exprs / sum_fpkm *1000000 +1\n",
"tpm.head()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"\n",
"tpm = tpm.applymap(np.log2)\n",
"#tpm.to_csv(preprocessed_data_dir + \"/PDX.FPKM2TPMplus1log2.Expr.tsv\",sep=\"\\t\")\n",
"print(tpm.shape)\n",
"tpm.head()\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# TCGA \n",
"\n",
"* from http://gdac.broadinstitute.org/runs/stddata__2016_01_18/data/ download RSEM files, \"scaled estimate\" per gene. \n",
"\n",
"* RSEM Scaled estimate is an aboundance of a transcript divided by sum of aboundance over all the transcripts. Therefore $TPM_i=ScaledEstimate_i*10^6$\n",
"\n",
"* Resulted TPM were log2-transformed"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"# replace with downloading \n",
"tcga_tmp_dir = \"/home/olya/SFU/Hossein/TCGA/expression__2016_01_28/\""
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"gdac.broadinstitute.org_BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 BRCA\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns 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have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"BRCA (20531, 1212)\n",
"gdac.broadinstitute.org_STES.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 STES\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512,514,515,517,518,520,521,523,524,526,527,529,530,532,533,535,536,538,539,541,542,544,545,547,548,550,551,553,554,556,557,559,560,562,563,565,566,568,569,571,572,574,575,577,578,580,581,583,584,586,587,589,590,592,593,595,596,598,599,601,602,604,605,607,608,610,611,613,614,616,617,619,620,622,623,625,626,628,629,631,632,634,635,637,638,640,641,643,644,646,647,649,650,652,653,655,656,658,659,661,662,664,665,667,668,670,671,673,674,676,677,679,680,682,683,685,686,688,689,691,692,694,695,697,698,700,701,703,704,706,707,709,710,712,713,715,716,718,719,721,722,724,725,727,728,730,731,733,734,736,737,739,740,742,743,745,746,748,749,751,752,754,755,757,758,760,761,763,764,766,767,769,770,772,773,775,776,778,779,781,782,784,785,787,788,790,791,793,794,796,797,799,800,802,803,805,806,808,809,811,812,814,815,817,818,820,821,823,824,826,827,829,830,832,833,835,836,838,839,841,842,844,845,847,848,850,851,853,854,856,857,859,860,862,863,865,866,868,869,871,872,874,875,877,878,880,881,883,884,886,887,889,890,892,893,895,896,898,899,901,902,904,905,907,908,910,911,913,914,916,917,919,920,922,923,925,926,928,929,931,932,934,935,937,938,940,941,943,944,946,947,949,950,952,953,955,956,958,959,961,962,964,965,967,968,970,971,973,974,976,977,979,980,982,983,985,986,988,989,991,992,994,995,997,998,1000,1001,1003,1004,1006,1007,1009,1010,1012,1013,1015,1016,1018,1019,1021,1022,1024,1025,1027,1028,1030,1031,1033,1034,1036,1037,1039,1040,1042,1043,1045,1046,1048,1049,1051,1052,1054,1055,1057,1058,1060,1061,1063,1064,1066,1067,1069,1070,1072,1073,1075,1076,1078,1079,1081,1082,1084,1085,1087,1088,1090,1091,1093,1094,1096,1097,1099,1100,1102,1103,1105,1106,1108,1109,1111,1112,1114,1115,1117,1118,1120,1121,1123,1124,1126,1127,1129,1130,1132,1133,1135,1136,1138,1139,1141,1142,1144,1145,1147,1148,1150,1151,1153,1154,1156,1157,1159,1160,1162,1163,1165,1166,1168,1169,1171,1172,1174,1175,1177,1178,1180,1181,1183,1184,1186,1187,1189,1190,1192,1193,1195,1196,1198,1199,1201,1202,1204,1205,1207,1208,1210,1211,1213,1214,1216,1217,1219,1220,1222,1223,1225,1226,1228,1229,1231,1232,1234,1235,1237,1238,1240,1241,1243,1244,1246,1247,1249,1250,1252,1253,1255,1256,1258,1259,1261,1262,1264,1265,1267,1268,1270,1271,1273,1274,1276,1277,1279,1280,1282,1283,1285,1286,1288,1289,1291,1292,1294,1295,1297,1298,1300,1301,1303,1304,1306,1307,1309,1310,1312,1313,1315,1316,1318,1319,1321,1322,1324,1325,1327,1328,1330,1331,1333,1334,1336,1337,1339,1340,1342,1343,1345,1346,1348,1349,1351,1352,1354,1355,1357,1358,1360,1361,1363,1364,1366,1367,1369,1370,1372,1373,1375,1376,1378,1379,1381,1382,1384,1385,1387,1388,1390,1391,1393,1394,1396,1397,1399,1400,1402,1403,1405,1406,1408,1409,1411,1412,1414,1415,1417,1418,1420,1421,1423,1424,1426,1427,1429,1430,1432,1433,1435,1436,1438,1439,1441,1442,1444,1445,1447,1448,1450,1451,1453,1454,1456,1457,1459,1460,1462,1463,1465,1466,1468,1469,1471,1472,1474,1475,1477,1478,1480,1481,1483,1484,1486,1487,1489,1490,1492,1493,1495,1496,1498,1499,1501,1502,1504,1505,1507,1508,1510,1511,1513,1514,1516,1517,1519,1520,1522,1523,1525,1526,1528,1529,1531,1532,1534,1535,1537,1538,1540,1541,1543,1544,1546,1547,1549,1550,1552,1553,1555,1556,1558,1559,1561,1562,1564,1565,1567,1568,1570,1571,1573,1574,1576,1577,1579,1580,1582,1583,1585,1586,1588,1589,1591,1592,1594,1595,1597,1598,1600,1601,1603,1604,1606,1607,1609,1610,1612,1613,1615,1616,1618,1619,1621,1622,1624,1625,1627,1628,1630,1631,1633,1634,1636,1637,1639,1640,1642,1643,1645,1646,1648,1649,1651,1652,1654,1655,1657,1658,1660,1661,1663,1664,1666,1667,1669,1670,1672,1673,1675,1676,1678,1679,1681,1682,1684,1685,1687,1688,1690,1691,1693,1694,1696,1697,1699,1700,1702,1703,1705,1706,1708,1709,1711,1712,1714,1715,1717,1718,1720,17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have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"STES (20531, 646)\n",
"gdac.broadinstitute.org_SKCM.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 SKCM\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512,514,515,517,518,520,521,523,524,526,527,529,530,532,533,535,536,538,539,541,542,544,545,547,548,550,551,553,554,556,557,559,560,562,563,565,566,568,569,571,572,574,575,577,578,580,581,583,584,586,587,589,590,592,593,595,596,598,599,601,602,604,605,607,608,610,611,613,614,616,617,619,620,622,623,625,626,628,629,631,632,634,635,637,638,640,641,643,644,646,647,649,650,652,653,655,656,658,659,661,662,664,665,667,668,670,671,673,674,676,677,679,680,682,683,685,686,688,689,691,692,694,695,697,698,700,701,703,704,706,707,709,710,712,713,715,716,718,719,721,722,724,725,727,728,730,731,733,734,736,737,739,740,742,743,745,746,748,749,751,752,754,755,757,758,760,761,763,764,766,767,769,770,772,773,775,776,778,779,781,782,784,785,787,788,790,791,793,794,796,797,799,800,802,803,805,806,808,809,811,812,814,815,817,818,820,821,823,824,826,827,829,830,832,833,835,836,838,839,841,842,844,845,847,848,850,851,853,854,856,857,859,860,862,863,865,866,868,869,871,872,874,875,877,878,880,881,883,884,886,887,889,890,892,893,895,896,898,899,901,902,904,905,907,908,910,911,913,914,916,917,919,920,922,923,925,926,928,929,931,932,934,935,937,938,940,941,943,944,946,947,949,950,952,953,955,956,958,959,961,962,964,965,967,968,970,971,973,974,976,977,979,980,982,983,985,986,988,989,991,992,994,995,997,998,1000,1001,1003,1004,1006,1007,1009,1010,1012,1013,1015,1016,1018,1019,1021,1022,1024,1025,1027,1028,1030,1031,1033,1034,1036,1037,1039,1040,1042,1043,1045,1046,1048,1049,1051,1052,1054,1055,1057,1058,1060,1061,1063,1064,1066,1067,1069,1070,1072,1073,1075,1076,1078,1079,1081,1082,1084,1085,1087,1088,1090,1091,1093,1094,1096,1097,1099,1100,1102,1103,1105,1106,1108,1109,1111,1112,1114,1115,1117,1118,1120,1121,1123,1124,1126,1127,1129,1130,1132,1133,1135,1136,1138,1139,1141,1142,1144,1145,1147,1148,1150,1151,1153,1154,1156,1157,1159,1160,1162,1163,1165,1166,1168,1169,1171,1172,1174,1175,1177,1178,1180,1181,1183,1184,1186,1187,1189,1190,1192,1193,1195,1196,1198,1199,1201,1202,1204,1205,1207,1208,1210,1211,1213,1214,1216,1217,1219,1220,1222,1223,1225,1226,1228,1229,1231,1232,1234,1235,1237,1238,1240,1241,1243,1244,1246,1247,1249,1250,1252,1253,1255,1256,1258,1259,1261,1262,1264,1265,1267,1268,1270,1271,1273,1274,1276,1277,1279,1280,1282,1283,1285,1286,1288,1289,1291,1292,1294,1295,1297,1298,1300,1301,1303,1304,1306,1307,1309,1310,1312,1313,1315,1316,1318,1319,1321,1322,1324,1325,1327,1328,1330,1331,1333,1334,1336,1337,1339,1340,1342,1343,1345,1346,1348,1349,1351,1352,1354,1355,1357,1358,1360,1361,1363,1364,1366,1367,1369,1370,1372,1373,1375,1376,1378,1379,1381,1382,1384,1385,1387,1388,1390,1391,1393,1394,1396,1397,1399,1400,1402,1403,1405,1406,1408,1409,1411,1412,1414,1415,1417,1418) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"SKCM (20531, 473)\n",
"gdac.broadinstitute.org_PAAD.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 PAAD\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512,514,515,517,518,520,521,523,524,526,527,529,530,532,533,535,536,538,539,541,542,544,545,547,548) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"PAAD (20531, 183)\n",
"gdac.broadinstitute.org_PCPG.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 PCPG\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512,514,515,517,518,520,521,523,524,526,527,529,530,532,533,535,536,538,539,541,542,544,545,547,548,550,551,553,554,556,557,559,560) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"PCPG (20531, 187)\n",
"gdac.broadinstitute.org_UCS.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 UCS\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
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{
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"UCS (20531, 57)\n",
"gdac.broadinstitute.org_THCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 THCA\n"
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"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512,514,515,517,518,520,521,523,524,526,527,529,530,532,533,535,536,538,539,541,542,544,545,547,548,550,551,553,554,556,557,559,560,562,563,565,566,568,569,571,572,574,575,577,578,580,581,583,584,586,587,589,590,592,593,595,596,598,599,601,602,604,605,607,608,610,611,613,614,616,617,619,620,622,623,625,626,628,629,631,632,634,635,637,638,640,641,643,644,646,647,649,650,652,653,655,656,658,659,661,662,664,665,667,668,670,671,673,674,676,677,679,680,682,683,685,686,688,689,691,692,694,695,697,698,700,701,703,704,706,707,709,710,712,713,715,716,718,719,721,722,724,725,727,728,730,731,733,734,736,737,739,740,742,743,745,746,748,749,751,752,754,755,757,758,760,761,763,764,766,767,769,770,772,773,775,776,778,779,781,782,784,785,787,788,790,791,793,794,796,797,799,800,802,803,805,806,808,809,811,812,814,815,817,818,820,821,823,824,826,827,829,830,832,833,835,836,838,839,841,842,844,845,847,848,850,851,853,854,856,857,859,860,862,863,865,866,868,869,871,872,874,875,877,878,880,881,883,884,886,887,889,890,892,893,895,896,898,899,901,902,904,905,907,908,910,911,913,914,916,917,919,920,922,923,925,926,928,929,931,932,934,935,937,938,940,941,943,944,946,947,949,950,952,953,955,956,958,959,961,962,964,965,967,968,970,971,973,974,976,977,979,980,982,983,985,986,988,989,991,992,994,995,997,998,1000,1001,1003,1004,1006,1007,1009,1010,1012,1013,1015,1016,1018,1019,1021,1022,1024,1025,1027,1028,1030,1031,1033,1034,1036,1037,1039,1040,1042,1043,1045,1046,1048,1049,1051,1052,1054,1055,1057,1058,1060,1061,1063,1064,1066,1067,1069,1070,1072,1073,1075,1076,1078,1079,1081,1082,1084,1085,1087,1088,1090,1091,1093,1094,1096,1097,1099,1100,1102,1103,1105,1106,1108,1109,1111,1112,1114,1115,1117,1118,1120,1121,1123,1124,1126,1127,1129,1130,1132,1133,1135,1136,1138,1139,1141,1142,1144,1145,1147,1148,1150,1151,1153,1154,1156,1157,1159,1160,1162,1163,1165,1166,1168,1169,1171,1172,1174,1175,1177,1178,1180,1181,1183,1184,1186,1187,1189,1190,1192,1193,1195,1196,1198,1199,1201,1202,1204,1205,1207,1208,1210,1211,1213,1214,1216,1217,1219,1220,1222,1223,1225,1226,1228,1229,1231,1232,1234,1235,1237,1238,1240,1241,1243,1244,1246,1247,1249,1250,1252,1253,1255,1256,1258,1259,1261,1262,1264,1265,1267,1268,1270,1271,1273,1274,1276,1277,1279,1280,1282,1283,1285,1286,1288,1289,1291,1292,1294,1295,1297,1298,1300,1301,1303,1304,1306,1307,1309,1310,1312,1313,1315,1316,1318,1319,1321,1322,1324,1325,1327,1328,1330,1331,1333,1334,1336,1337,1339,1340,1342,1343,1345,1346,1348,1349,1351,1352,1354,1355,1357,1358,1360,1361,1363,1364,1366,1367,1369,1370,1372,1373,1375,1376,1378,1379,1381,1382,1384,1385,1387,1388,1390,1391,1393,1394,1396,1397,1399,1400,1402,1403,1405,1406,1408,1409,1411,1412,1414,1415,1417,1418,1420,1421,1423,1424,1426,1427,1429,1430,1432,1433,1435,1436,1438,1439,1441,1442,1444,1445,1447,1448,1450,1451,1453,1454,1456,1457,1459,1460,1462,1463,1465,1466,1468,1469,1471,1472,1474,1475,1477,1478,1480,1481,1483,1484,1486,1487,1489,1490,1492,1493,1495,1496,1498,1499,1501,1502,1504,1505,1507,1508,1510,1511,1513,1514,1516,1517,1519,1520,1522,1523,1525,1526,1528,1529,1531,1532,1534,1535,1537,1538,1540,1541,1543,1544,1546,1547,1549,1550,1552,1553,1555,1556,1558,1559,1561,1562,1564,1565,1567,1568,1570,1571,1573,1574,1576,1577,1579,1580,1582,1583,1585,1586,1588,1589,1591,1592,1594,1595,1597,1598,1600,1601,1603,1604,1606,1607,1609,1610,1612,1613,1615,1616,1618,1619,1621,1622,1624,1625,1627,1628,1630,1631,1633,1634,1636,1637,1639,1640,1642,1643,1645,1646,1648,1649,1651,1652,1654,1655,1657,1658,1660,1661,1663,1664,1666,1667,1669,1670,1672,1673,1675,1676,1678,1679,1681,1682,1684,1685,1687,1688,1690,1691,1693,1694,1696,1697,1699,1700,1702,1703) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"THCA (20531, 568)\n",
"gdac.broadinstitute.org_CESC.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 CESC\n"
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"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512,514,515,517,518,520,521,523,524,526,527,529,530,532,533,535,536,538,539,541,542,544,545,547,548,550,551,553,554,556,557,559,560,562,563,565,566,568,569,571,572,574,575,577,578,580,581,583,584,586,587,589,590,592,593,595,596,598,599,601,602,604,605,607,608,610,611,613,614,616,617,619,620,622,623,625,626,628,629,631,632,634,635,637,638,640,641,643,644,646,647,649,650,652,653,655,656,658,659,661,662,664,665,667,668,670,671,673,674,676,677,679,680,682,683,685,686,688,689,691,692,694,695,697,698,700,701,703,704,706,707,709,710,712,713,715,716,718,719,721,722,724,725,727,728,730,731,733,734,736,737,739,740,742,743,745,746,748,749,751,752,754,755,757,758,760,761,763,764,766,767,769,770,772,773,775,776,778,779,781,782,784,785,787,788,790,791,793,794,796,797,799,800,802,803,805,806,808,809,811,812,814,815,817,818,820,821,823,824,826,827,829,830,832,833,835,836,838,839,841,842,844,845,847,848,850,851,853,854,856,857,859,860,862,863,865,866,868,869,871,872,874,875,877,878,880,881,883,884,886,887,889,890,892,893,895,896,898,899,901,902,904,905,907,908,910,911,913,914,916,917,919,920,922,923,925,926) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
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{
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"text": [
"CESC (20531, 309)\n",
"gdac.broadinstitute.org_KIRP.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 KIRP\n"
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"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512,514,515,517,518,520,521,523,524,526,527,529,530,532,533,535,536,538,539,541,542,544,545,547,548,550,551,553,554,556,557,559,560,562,563,565,566,568,569,571,572,574,575,577,578,580,581,583,584,586,587,589,590,592,593,595,596,598,599,601,602,604,605,607,608,610,611,613,614,616,617,619,620,622,623,625,626,628,629,631,632,634,635,637,638,640,641,643,644,646,647,649,650,652,653,655,656,658,659,661,662,664,665,667,668,670,671,673,674,676,677,679,680,682,683,685,686,688,689,691,692,694,695,697,698,700,701,703,704,706,707,709,710,712,713,715,716,718,719,721,722,724,725,727,728,730,731,733,734,736,737,739,740,742,743,745,746,748,749,751,752,754,755,757,758,760,761,763,764,766,767,769,770,772,773,775,776,778,779,781,782,784,785,787,788,790,791,793,794,796,797,799,800,802,803,805,806,808,809,811,812,814,815,817,818,820,821,823,824,826,827,829,830,832,833,835,836,838,839,841,842,844,845,847,848,850,851,853,854,856,857,859,860,862,863,865,866,868,869,871,872,874,875,877,878,880,881,883,884,886,887,889,890,892,893,895,896,898,899,901,902,904,905,907,908,910,911,913,914,916,917,919,920,922,923,925,926,928,929,931,932,934,935,937,938,940,941,943,944,946,947,949,950,952,953,955,956,958,959,961,962,964,965,967,968) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
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"text": [
"KIRP (20531, 323)\n",
"gdac.broadinstitute.org_COAD.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 COAD\n"
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"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512,514,515,517,518,520,521,523,524,526,527,529,530,532,533,535,536,538,539,541,542,544,545,547,548,550,551,553,554,556,557,559,560,562,563,565,566,568,569,571,572,574,575,577,578,580,581,583,584,586,587,589,590,592,593,595,596,598,599,601,602,604,605,607,608,610,611,613,614,616,617,619,620,622,623,625,626,628,629,631,632,634,635,637,638,640,641,643,644,646,647,649,650,652,653,655,656,658,659,661,662,664,665,667,668,670,671,673,674,676,677,679,680,682,683,685,686,688,689,691,692,694,695,697,698,700,701,703,704,706,707,709,710,712,713,715,716,718,719,721,722,724,725,727,728,730,731,733,734,736,737,739,740,742,743,745,746,748,749,751,752,754,755,757,758,760,761,763,764,766,767,769,770,772,773,775,776,778,779,781,782,784,785,787,788,790,791,793,794,796,797,799,800,802,803,805,806,808,809,811,812,814,815,817,818,820,821,823,824,826,827,829,830,832,833,835,836,838,839,841,842,844,845,847,848,850,851,853,854,856,857,859,860,862,863,865,866,868,869,871,872,874,875,877,878,880,881,883,884,886,887,889,890,892,893,895,896,898,899,901,902,904,905,907,908,910,911,913,914,916,917,919,920,922,923,925,926,928,929,931,932,934,935,937,938,940,941,943,944,946,947,949,950,952,953,955,956,958,959,961,962,964,965,967,968,970,971,973,974,976,977,979,980,982,983) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
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{
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"output_type": "stream",
"text": [
"COAD (20531, 328)\n",
"gdac.broadinstitute.org_KIRC.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 KIRC\n"
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"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512,514,515,517,518,520,521,523,524,526,527,529,530,532,533,535,536,538,539,541,542,544,545,547,548,550,551,553,554,556,557,559,560,562,563,565,566,568,569,571,572,574,575,577,578,580,581,583,584,586,587,589,590,592,593,595,596,598,599,601,602,604,605,607,608,610,611,613,614,616,617,619,620,622,623,625,626,628,629,631,632,634,635,637,638,640,641,643,644,646,647,649,650,652,653,655,656,658,659,661,662,664,665,667,668,670,671,673,674,676,677,679,680,682,683,685,686,688,689,691,692,694,695,697,698,700,701,703,704,706,707,709,710,712,713,715,716,718,719,721,722,724,725,727,728,730,731,733,734,736,737,739,740,742,743,745,746,748,749,751,752,754,755,757,758,760,761,763,764,766,767,769,770,772,773,775,776,778,779,781,782,784,785,787,788,790,791,793,794,796,797,799,800,802,803,805,806,808,809,811,812,814,815,817,818,820,821,823,824,826,827,829,830,832,833,835,836,838,839,841,842,844,845,847,848,850,851,853,854,856,857,859,860,862,863,865,866,868,869,871,872,874,875,877,878,880,881,883,884,886,887,889,890,892,893,895,896,898,899,901,902,904,905,907,908,910,911,913,914,916,917,919,920,922,923,925,926,928,929,931,932,934,935,937,938,940,941,943,944,946,947,949,950,952,953,955,956,958,959,961,962,964,965,967,968,970,971,973,974,976,977,979,980,982,983,985,986,988,989,991,992,994,995,997,998,1000,1001,1003,1004,1006,1007,1009,1010,1012,1013,1015,1016,1018,1019,1021,1022,1024,1025,1027,1028,1030,1031,1033,1034,1036,1037,1039,1040,1042,1043,1045,1046,1048,1049,1051,1052,1054,1055,1057,1058,1060,1061,1063,1064,1066,1067,1069,1070,1072,1073,1075,1076,1078,1079,1081,1082,1084,1085,1087,1088,1090,1091,1093,1094,1096,1097,1099,1100,1102,1103,1105,1106,1108,1109,1111,1112,1114,1115,1117,1118,1120,1121,1123,1124,1126,1127,1129,1130,1132,1133,1135,1136,1138,1139,1141,1142,1144,1145,1147,1148,1150,1151,1153,1154,1156,1157,1159,1160,1162,1163,1165,1166,1168,1169,1171,1172,1174,1175,1177,1178,1180,1181,1183,1184,1186,1187,1189,1190,1192,1193,1195,1196,1198,1199,1201,1202,1204,1205,1207,1208,1210,1211,1213,1214,1216,1217,1219,1220,1222,1223,1225,1226,1228,1229,1231,1232,1234,1235,1237,1238,1240,1241,1243,1244,1246,1247,1249,1250,1252,1253,1255,1256,1258,1259,1261,1262,1264,1265,1267,1268,1270,1271,1273,1274,1276,1277,1279,1280,1282,1283,1285,1286,1288,1289,1291,1292,1294,1295,1297,1298,1300,1301,1303,1304,1306,1307,1309,1310,1312,1313,1315,1316,1318,1319,1321,1322,1324,1325,1327,1328,1330,1331,1333,1334,1336,1337,1339,1340,1342,1343,1345,1346,1348,1349,1351,1352,1354,1355,1357,1358,1360,1361,1363,1364,1366,1367,1369,1370,1372,1373,1375,1376,1378,1379,1381,1382,1384,1385,1387,1388,1390,1391,1393,1394,1396,1397,1399,1400,1402,1403,1405,1406,1408,1409,1411,1412,1414,1415,1417,1418,1420,1421,1423,1424,1426,1427,1429,1430,1432,1433,1435,1436,1438,1439,1441,1442,1444,1445,1447,1448,1450,1451,1453,1454,1456,1457,1459,1460,1462,1463,1465,1466,1468,1469,1471,1472,1474,1475,1477,1478,1480,1481,1483,1484,1486,1487,1489,1490,1492,1493,1495,1496,1498,1499,1501,1502,1504,1505,1507,1508,1510,1511,1513,1514,1516,1517,1519,1520,1522,1523,1525,1526,1528,1529,1531,1532,1534,1535,1537,1538,1540,1541,1543,1544,1546,1547,1549,1550,1552,1553,1555,1556,1558,1559,1561,1562,1564,1565,1567,1568,1570,1571,1573,1574,1576,1577,1579,1580,1582,1583,1585,1586,1588,1589,1591,1592,1594,1595,1597,1598,1600,1601,1603,1604,1606,1607,1609,1610,1612,1613,1615,1616,1618,1619,1621,1622,1624,1625,1627,1628,1630,1631,1633,1634,1636,1637,1639,1640,1642,1643,1645,1646,1648,1649,1651,1652,1654,1655,1657,1658,1660,1661,1663,1664,1666,1667,1669,1670,1672,1673,1675,1676,1678,1679,1681,1682,1684,1685,1687,1688,1690,1691,1693,1694,1696,1697,1699,1700,1702,1703,1705,1706,1708,1709,1711,1712,1714,1715,1717,1718,1720,1721,1723,1724,1726,1727,1729,1730,1732,1733,1735,1736,1738,1739,1741,1742,1744,1745,1747,1748,1750,1751,1753,1754,1756,1757,1759,1760,1762,1763,1765,1766,1768,1769,1771,1772,1774,1775,1777,1778,1780,1781,1783,1784,1786,1787,1789,1790,1792,1793,1795,1796,1798,1799,1801,1802,1804,1805,1807,1808,1810,1811,1813,1814,1816,1817) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"KIRC (20531, 606)\n",
"gdac.broadinstitute.org_THYM.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 THYM\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"THYM (20531, 122)\n",
"gdac.broadinstitute.org_LIHC.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 LIHC\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512,514,515,517,518,520,521,523,524,526,527,529,530,532,533,535,536,538,539,541,542,544,545,547,548,550,551,553,554,556,557,559,560,562,563,565,566,568,569,571,572,574,575,577,578,580,581,583,584,586,587,589,590,592,593,595,596,598,599,601,602,604,605,607,608,610,611,613,614,616,617,619,620,622,623,625,626,628,629,631,632,634,635,637,638,640,641,643,644,646,647,649,650,652,653,655,656,658,659,661,662,664,665,667,668,670,671,673,674,676,677,679,680,682,683,685,686,688,689,691,692,694,695,697,698,700,701,703,704,706,707,709,710,712,713,715,716,718,719,721,722,724,725,727,728,730,731,733,734,736,737,739,740,742,743,745,746,748,749,751,752,754,755,757,758,760,761,763,764,766,767,769,770,772,773,775,776,778,779,781,782,784,785,787,788,790,791,793,794,796,797,799,800,802,803,805,806,808,809,811,812,814,815,817,818,820,821,823,824,826,827,829,830,832,833,835,836,838,839,841,842,844,845,847,848,850,851,853,854,856,857,859,860,862,863,865,866,868,869,871,872,874,875,877,878,880,881,883,884,886,887,889,890,892,893,895,896,898,899,901,902,904,905,907,908,910,911,913,914,916,917,919,920,922,923,925,926,928,929,931,932,934,935,937,938,940,941,943,944,946,947,949,950,952,953,955,956,958,959,961,962,964,965,967,968,970,971,973,974,976,977,979,980,982,983,985,986,988,989,991,992,994,995,997,998,1000,1001,1003,1004,1006,1007,1009,1010,1012,1013,1015,1016,1018,1019,1021,1022,1024,1025,1027,1028,1030,1031,1033,1034,1036,1037,1039,1040,1042,1043,1045,1046,1048,1049,1051,1052,1054,1055,1057,1058,1060,1061,1063,1064,1066,1067,1069,1070,1072,1073,1075,1076,1078,1079,1081,1082,1084,1085,1087,1088,1090,1091,1093,1094,1096,1097,1099,1100,1102,1103,1105,1106,1108,1109,1111,1112,1114,1115,1117,1118,1120,1121,1123,1124,1126,1127,1129,1130,1132,1133,1135,1136,1138,1139,1141,1142,1144,1145,1147,1148,1150,1151,1153,1154,1156,1157,1159,1160,1162,1163,1165,1166,1168,1169,1171,1172,1174,1175,1177,1178,1180,1181,1183,1184,1186,1187,1189,1190,1192,1193,1195,1196,1198,1199,1201,1202,1204,1205,1207,1208,1210,1211,1213,1214,1216,1217,1219,1220,1222,1223,1225,1226,1228,1229,1231,1232,1234,1235,1237,1238,1240,1241,1243,1244,1246,1247,1249,1250,1252,1253,1255,1256,1258,1259,1261,1262,1264,1265,1267,1268) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"LIHC (20531, 423)\n",
"gdac.broadinstitute.org_READ.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 READ\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"READ (20531, 105)\n",
"gdac.broadinstitute.org_GBM.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 GBM\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"GBM (20531, 171)\n",
"gdac.broadinstitute.org_LUAD.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 LUAD\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512,514,515,517,518,520,521,523,524,526,527,529,530,532,533,535,536,538,539,541,542,544,545,547,548,550,551,553,554,556,557,559,560,562,563,565,566,568,569,571,572,574,575,577,578,580,581,583,584,586,587,589,590,592,593,595,596,598,599,601,602,604,605,607,608,610,611,613,614,616,617,619,620,622,623,625,626,628,629,631,632,634,635,637,638,640,641,643,644,646,647,649,650,652,653,655,656,658,659,661,662,664,665,667,668,670,671,673,674,676,677,679,680,682,683,685,686,688,689,691,692,694,695,697,698,700,701,703,704,706,707,709,710,712,713,715,716,718,719,721,722,724,725,727,728,730,731,733,734,736,737,739,740,742,743,745,746,748,749,751,752,754,755,757,758,760,761,763,764,766,767,769,770,772,773,775,776,778,779,781,782,784,785,787,788,790,791,793,794,796,797,799,800,802,803,805,806,808,809,811,812,814,815,817,818,820,821,823,824,826,827,829,830,832,833,835,836,838,839,841,842,844,845,847,848,850,851,853,854,856,857,859,860,862,863,865,866,868,869,871,872,874,875,877,878,880,881,883,884,886,887,889,890,892,893,895,896,898,899,901,902,904,905,907,908,910,911,913,914,916,917,919,920,922,923,925,926,928,929,931,932,934,935,937,938,940,941,943,944,946,947,949,950,952,953,955,956,958,959,961,962,964,965,967,968,970,971,973,974,976,977,979,980,982,983,985,986,988,989,991,992,994,995,997,998,1000,1001,1003,1004,1006,1007,1009,1010,1012,1013,1015,1016,1018,1019,1021,1022,1024,1025,1027,1028,1030,1031,1033,1034,1036,1037,1039,1040,1042,1043,1045,1046,1048,1049,1051,1052,1054,1055,1057,1058,1060,1061,1063,1064,1066,1067,1069,1070,1072,1073,1075,1076,1078,1079,1081,1082,1084,1085,1087,1088,1090,1091,1093,1094,1096,1097,1099,1100,1102,1103,1105,1106,1108,1109,1111,1112,1114,1115,1117,1118,1120,1121,1123,1124,1126,1127,1129,1130,1132,1133,1135,1136,1138,1139,1141,1142,1144,1145,1147,1148,1150,1151,1153,1154,1156,1157,1159,1160,1162,1163,1165,1166,1168,1169,1171,1172,1174,1175,1177,1178,1180,1181,1183,1184,1186,1187,1189,1190,1192,1193,1195,1196,1198,1199,1201,1202,1204,1205,1207,1208,1210,1211,1213,1214,1216,1217,1219,1220,1222,1223,1225,1226,1228,1229,1231,1232,1234,1235,1237,1238,1240,1241,1243,1244,1246,1247,1249,1250,1252,1253,1255,1256,1258,1259,1261,1262,1264,1265,1267,1268,1270,1271,1273,1274,1276,1277,1279,1280,1282,1283,1285,1286,1288,1289,1291,1292,1294,1295,1297,1298,1300,1301,1303,1304,1306,1307,1309,1310,1312,1313,1315,1316,1318,1319,1321,1322,1324,1325,1327,1328,1330,1331,1333,1334,1336,1337,1339,1340,1342,1343,1345,1346,1348,1349,1351,1352,1354,1355,1357,1358,1360,1361,1363,1364,1366,1367,1369,1370,1372,1373,1375,1376,1378,1379,1381,1382,1384,1385,1387,1388,1390,1391,1393,1394,1396,1397,1399,1400,1402,1403,1405,1406,1408,1409,1411,1412,1414,1415,1417,1418,1420,1421,1423,1424,1426,1427,1429,1430,1432,1433,1435,1436,1438,1439,1441,1442,1444,1445,1447,1448,1450,1451,1453,1454,1456,1457,1459,1460,1462,1463,1465,1466,1468,1469,1471,1472,1474,1475,1477,1478,1480,1481,1483,1484,1486,1487,1489,1490,1492,1493,1495,1496,1498,1499,1501,1502,1504,1505,1507,1508,1510,1511,1513,1514,1516,1517,1519,1520,1522,1523,1525,1526,1528,1529,1531,1532,1534,1535,1537,1538,1540,1541,1543,1544,1546,1547,1549,1550,1552,1553,1555,1556,1558,1559,1561,1562,1564,1565,1567,1568,1570,1571,1573,1574,1576,1577,1579,1580,1582,1583,1585,1586,1588,1589,1591,1592,1594,1595,1597,1598,1600,1601,1603,1604,1606,1607,1609,1610,1612,1613,1615,1616,1618,1619,1621,1622,1624,1625,1627,1628,1630,1631,1633,1634,1636,1637,1639,1640,1642,1643,1645,1646,1648,1649,1651,1652,1654,1655,1657,1658,1660,1661,1663,1664,1666,1667,1669,1670,1672,1673,1675,1676,1678,1679,1681,1682,1684,1685,1687,1688,1690,1691,1693,1694,1696,1697,1699,1700,1702,1703,1705,1706,1708,1709,1711,1712,1714,1715,1717,1718,1720,17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have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"LUAD (20531, 576)\n",
"gdac.broadinstitute.org_DLBC.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 DLBC\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"DLBC (20531, 48)\n",
"gdac.broadinstitute.org_KICH.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 KICH\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"KICH (20531, 91)\n",
"gdac.broadinstitute.org_CHOL.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 CHOL\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"CHOL (20531, 45)\n",
"gdac.broadinstitute.org_UVM.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 UVM\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"UVM (20531, 80)\n",
"gdac.broadinstitute.org_PRAD.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 PRAD\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512,514,515,517,518,520,521,523,524,526,527,529,530,532,533,535,536,538,539,541,542,544,545,547,548,550,551,553,554,556,557,559,560,562,563,565,566,568,569,571,572,574,575,577,578,580,581,583,584,586,587,589,590,592,593,595,596,598,599,601,602,604,605,607,608,610,611,613,614,616,617,619,620,622,623,625,626,628,629,631,632,634,635,637,638,640,641,643,644,646,647,649,650,652,653,655,656,658,659,661,662,664,665,667,668,670,671,673,674,676,677,679,680,682,683,685,686,688,689,691,692,694,695,697,698,700,701,703,704,706,707,709,710,712,713,715,716,718,719,721,722,724,725,727,728,730,731,733,734,736,737,739,740,742,743,745,746,748,749,751,752,754,755,757,758,760,761,763,764,766,767,769,770,772,773,775,776,778,779,781,782,784,785,787,788,790,791,793,794,796,797,799,800,802,803,805,806,808,809,811,812,814,815,817,818,820,821,823,824,826,827,829,830,832,833,835,836,838,839,841,842,844,845,847,848,850,851,853,854,856,857,859,860,862,863,865,866,868,869,871,872,874,875,877,878,880,881,883,884,886,887,889,890,892,893,895,896,898,899,901,902,904,905,907,908,910,911,913,914,916,917,919,920,922,923,925,926,928,929,931,932,934,935,937,938,940,941,943,944,946,947,949,950,952,953,955,956,958,959,961,962,964,965,967,968,970,971,973,974,976,977,979,980,982,983,985,986,988,989,991,992,994,995,997,998,1000,1001,1003,1004,1006,1007,1009,1010,1012,1013,1015,1016,1018,1019,1021,1022,1024,1025,1027,1028,1030,1031,1033,1034,1036,1037,1039,1040,1042,1043,1045,1046,1048,1049,1051,1052,1054,1055,1057,1058,1060,1061,1063,1064,1066,1067,1069,1070,1072,1073,1075,1076,1078,1079,1081,1082,1084,1085,1087,1088,1090,1091,1093,1094,1096,1097,1099,1100,1102,1103,1105,1106,1108,1109,1111,1112,1114,1115,1117,1118,1120,1121,1123,1124,1126,1127,1129,1130,1132,1133,1135,1136,1138,1139,1141,1142,1144,1145,1147,1148,1150,1151,1153,1154,1156,1157,1159,1160,1162,1163,1165,1166,1168,1169,1171,1172,1174,1175,1177,1178,1180,1181,1183,1184,1186,1187,1189,1190,1192,1193,1195,1196,1198,1199,1201,1202,1204,1205,1207,1208,1210,1211,1213,1214,1216,1217,1219,1220,1222,1223,1225,1226,1228,1229,1231,1232,1234,1235,1237,1238,1240,1241,1243,1244,1246,1247,1249,1250,1252,1253,1255,1256,1258,1259,1261,1262,1264,1265,1267,1268,1270,1271,1273,1274,1276,1277,1279,1280,1282,1283,1285,1286,1288,1289,1291,1292,1294,1295,1297,1298,1300,1301,1303,1304,1306,1307,1309,1310,1312,1313,1315,1316,1318,1319,1321,1322,1324,1325,1327,1328,1330,1331,1333,1334,1336,1337,1339,1340,1342,1343,1345,1346,1348,1349,1351,1352,1354,1355,1357,1358,1360,1361,1363,1364,1366,1367,1369,1370,1372,1373,1375,1376,1378,1379,1381,1382,1384,1385,1387,1388,1390,1391,1393,1394,1396,1397,1399,1400,1402,1403,1405,1406,1408,1409,1411,1412,1414,1415,1417,1418,1420,1421,1423,1424,1426,1427,1429,1430,1432,1433,1435,1436,1438,1439,1441,1442,1444,1445,1447,1448,1450,1451,1453,1454,1456,1457,1459,1460,1462,1463,1465,1466,1468,1469,1471,1472,1474,1475,1477,1478,1480,1481,1483,1484,1486,1487,1489,1490,1492,1493,1495,1496,1498,1499,1501,1502,1504,1505,1507,1508,1510,1511,1513,1514,1516,1517,1519,1520,1522,1523,1525,1526,1528,1529,1531,1532,1534,1535,1537,1538,1540,1541,1543,1544,1546,1547,1549,1550,1552,1553,1555,1556,1558,1559,1561,1562,1564,1565,1567,1568,1570,1571,1573,1574,1576,1577,1579,1580,1582,1583,1585,1586,1588,1589,1591,1592,1594,1595,1597,1598,1600,1601,1603,1604,1606,1607,1609,1610,1612,1613,1615,1616,1618,1619,1621,1622,1624,1625,1627,1628,1630,1631,1633,1634,1636,1637,1639,1640,1642,1643,1645,1646,1648,1649) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"PRAD (20531, 550)\n",
"gdac.broadinstitute.org_UCEC.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 UCEC\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512,514,515,517,518,520,521,523,524,526,527,529,530,532,533,535,536,538,539,541,542,544,545,547,548,550,551,553,554,556,557,559,560,562,563,565,566,568,569,571,572,574,575,577,578,580,581,583,584,586,587,589,590,592,593,595,596,598,599,601,602) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"UCEC (20531, 201)\n",
"gdac.broadinstitute.org_SARC.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 SARC\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512,514,515,517,518,520,521,523,524,526,527,529,530,532,533,535,536,538,539,541,542,544,545,547,548,550,551,553,554,556,557,559,560,562,563,565,566,568,569,571,572,574,575,577,578,580,581,583,584,586,587,589,590,592,593,595,596,598,599,601,602,604,605,607,608,610,611,613,614,616,617,619,620,622,623,625,626,628,629,631,632,634,635,637,638,640,641,643,644,646,647,649,650,652,653,655,656,658,659,661,662,664,665,667,668,670,671,673,674,676,677,679,680,682,683,685,686,688,689,691,692,694,695,697,698,700,701,703,704,706,707,709,710,712,713,715,716,718,719,721,722,724,725,727,728,730,731,733,734,736,737,739,740,742,743,745,746,748,749,751,752,754,755,757,758,760,761,763,764,766,767,769,770,772,773,775,776,778,779,781,782,784,785,787,788,790,791,793,794) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"SARC (20531, 265)\n",
"gdac.broadinstitute.org_TGCT.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 TGCT\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"TGCT (20531, 156)\n",
"gdac.broadinstitute.org_LGG.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 LGG\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512,514,515,517,518,520,521,523,524,526,527,529,530,532,533,535,536,538,539,541,542,544,545,547,548,550,551,553,554,556,557,559,560,562,563,565,566,568,569,571,572,574,575,577,578,580,581,583,584,586,587,589,590,592,593,595,596,598,599,601,602,604,605,607,608,610,611,613,614,616,617,619,620,622,623,625,626,628,629,631,632,634,635,637,638,640,641,643,644,646,647,649,650,652,653,655,656,658,659,661,662,664,665,667,668,670,671,673,674,676,677,679,680,682,683,685,686,688,689,691,692,694,695,697,698,700,701,703,704,706,707,709,710,712,713,715,716,718,719,721,722,724,725,727,728,730,731,733,734,736,737,739,740,742,743,745,746,748,749,751,752,754,755,757,758,760,761,763,764,766,767,769,770,772,773,775,776,778,779,781,782,784,785,787,788,790,791,793,794,796,797,799,800,802,803,805,806,808,809,811,812,814,815,817,818,820,821,823,824,826,827,829,830,832,833,835,836,838,839,841,842,844,845,847,848,850,851,853,854,856,857,859,860,862,863,865,866,868,869,871,872,874,875,877,878,880,881,883,884,886,887,889,890,892,893,895,896,898,899,901,902,904,905,907,908,910,911,913,914,916,917,919,920,922,923,925,926,928,929,931,932,934,935,937,938,940,941,943,944,946,947,949,950,952,953,955,956,958,959,961,962,964,965,967,968,970,971,973,974,976,977,979,980,982,983,985,986,988,989,991,992,994,995,997,998,1000,1001,1003,1004,1006,1007,1009,1010,1012,1013,1015,1016,1018,1019,1021,1022,1024,1025,1027,1028,1030,1031,1033,1034,1036,1037,1039,1040,1042,1043,1045,1046,1048,1049,1051,1052,1054,1055,1057,1058,1060,1061,1063,1064,1066,1067,1069,1070,1072,1073,1075,1076,1078,1079,1081,1082,1084,1085,1087,1088,1090,1091,1093,1094,1096,1097,1099,1100,1102,1103,1105,1106,1108,1109,1111,1112,1114,1115,1117,1118,1120,1121,1123,1124,1126,1127,1129,1130,1132,1133,1135,1136,1138,1139,1141,1142,1144,1145,1147,1148,1150,1151,1153,1154,1156,1157,1159,1160,1162,1163,1165,1166,1168,1169,1171,1172,1174,1175,1177,1178,1180,1181,1183,1184,1186,1187,1189,1190,1192,1193,1195,1196,1198,1199,1201,1202,1204,1205,1207,1208,1210,1211,1213,1214,1216,1217,1219,1220,1222,1223,1225,1226,1228,1229,1231,1232,1234,1235,1237,1238,1240,1241,1243,1244,1246,1247,1249,1250,1252,1253,1255,1256,1258,1259,1261,1262,1264,1265,1267,1268,1270,1271,1273,1274,1276,1277,1279,1280,1282,1283,1285,1286,1288,1289,1291,1292,1294,1295,1297,1298,1300,1301,1303,1304,1306,1307,1309,1310,1312,1313,1315,1316,1318,1319,1321,1322,1324,1325,1327,1328,1330,1331,1333,1334,1336,1337,1339,1340,1342,1343,1345,1346,1348,1349,1351,1352,1354,1355,1357,1358,1360,1361,1363,1364,1366,1367,1369,1370,1372,1373,1375,1376,1378,1379,1381,1382,1384,1385,1387,1388,1390,1391,1393,1394,1396,1397,1399,1400,1402,1403,1405,1406,1408,1409,1411,1412,1414,1415,1417,1418,1420,1421,1423,1424,1426,1427,1429,1430,1432,1433,1435,1436,1438,1439,1441,1442,1444,1445,1447,1448,1450,1451,1453,1454,1456,1457,1459,1460,1462,1463,1465,1466,1468,1469,1471,1472,1474,1475,1477,1478,1480,1481,1483,1484,1486,1487,1489,1490,1492,1493,1495,1496,1498,1499,1501,1502,1504,1505,1507,1508,1510,1511,1513,1514,1516,1517,1519,1520,1522,1523,1525,1526,1528,1529,1531,1532,1534,1535,1537,1538,1540,1541,1543,1544,1546,1547,1549,1550,1552,1553,1555,1556,1558,1559,1561,1562,1564,1565,1567,1568,1570,1571,1573,1574,1576,1577,1579,1580,1582,1583,1585,1586,1588,1589) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"LGG (20531, 530)\n",
"gdac.broadinstitute.org_ESCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 ESCA\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512,514,515,517,518,520,521,523,524,526,527,529,530,532,533,535,536,538,539,541,542,544,545,547,548,550,551,553,554,556,557,559,560,562,563,565,566,568,569,571,572,574,575,577,578,580,581,583,584,586,587) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"ESCA (20531, 196)\n",
"gdac.broadinstitute.org_ACC.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 ACC\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"ACC (20531, 79)\n",
"gdac.broadinstitute.org_LAML.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 LAML\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512,514,515,517,518) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"LAML (20531, 173)\n",
"gdac.broadinstitute.org_HNSC.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 HNSC\n"
]
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"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512,514,515,517,518,520,521,523,524,526,527,529,530,532,533,535,536,538,539,541,542,544,545,547,548,550,551,553,554,556,557,559,560,562,563,565,566,568,569,571,572,574,575,577,578,580,581,583,584,586,587,589,590,592,593,595,596,598,599,601,602,604,605,607,608,610,611,613,614,616,617,619,620,622,623,625,626,628,629,631,632,634,635,637,638,640,641,643,644,646,647,649,650,652,653,655,656,658,659,661,662,664,665,667,668,670,671,673,674,676,677,679,680,682,683,685,686,688,689,691,692,694,695,697,698,700,701,703,704,706,707,709,710,712,713,715,716,718,719,721,722,724,725,727,728,730,731,733,734,736,737,739,740,742,743,745,746,748,749,751,752,754,755,757,758,760,761,763,764,766,767,769,770,772,773,775,776,778,779,781,782,784,785,787,788,790,791,793,794,796,797,799,800,802,803,805,806,808,809,811,812,814,815,817,818,820,821,823,824,826,827,829,830,832,833,835,836,838,839,841,842,844,845,847,848,850,851,853,854,856,857,859,860,862,863,865,866,868,869,871,872,874,875,877,878,880,881,883,884,886,887,889,890,892,893,895,896,898,899,901,902,904,905,907,908,910,911,913,914,916,917,919,920,922,923,925,926,928,929,931,932,934,935,937,938,940,941,943,944,946,947,949,950,952,953,955,956,958,959,961,962,964,965,967,968,970,971,973,974,976,977,979,980,982,983,985,986,988,989,991,992,994,995,997,998,1000,1001,1003,1004,1006,1007,1009,1010,1012,1013,1015,1016,1018,1019,1021,1022,1024,1025,1027,1028,1030,1031,1033,1034,1036,1037,1039,1040,1042,1043,1045,1046,1048,1049,1051,1052,1054,1055,1057,1058,1060,1061,1063,1064,1066,1067,1069,1070,1072,1073,1075,1076,1078,1079,1081,1082,1084,1085,1087,1088,1090,1091,1093,1094,1096,1097,1099,1100,1102,1103,1105,1106,1108,1109,1111,1112,1114,1115,1117,1118,1120,1121,1123,1124,1126,1127,1129,1130,1132,1133,1135,1136,1138,1139,1141,1142,1144,1145,1147,1148,1150,1151,1153,1154,1156,1157,1159,1160,1162,1163,1165,1166,1168,1169,1171,1172,1174,1175,1177,1178,1180,1181,1183,1184,1186,1187,1189,1190,1192,1193,1195,1196,1198,1199,1201,1202,1204,1205,1207,1208,1210,1211,1213,1214,1216,1217,1219,1220,1222,1223,1225,1226,1228,1229,1231,1232,1234,1235,1237,1238,1240,1241,1243,1244,1246,1247,1249,1250,1252,1253,1255,1256,1258,1259,1261,1262,1264,1265,1267,1268,1270,1271,1273,1274,1276,1277,1279,1280,1282,1283,1285,1286,1288,1289,1291,1292,1294,1295,1297,1298,1300,1301,1303,1304,1306,1307,1309,1310,1312,1313,1315,1316,1318,1319,1321,1322,1324,1325,1327,1328,1330,1331,1333,1334,1336,1337,1339,1340,1342,1343,1345,1346,1348,1349,1351,1352,1354,1355,1357,1358,1360,1361,1363,1364,1366,1367,1369,1370,1372,1373,1375,1376,1378,1379,1381,1382,1384,1385,1387,1388,1390,1391,1393,1394,1396,1397,1399,1400,1402,1403,1405,1406,1408,1409,1411,1412,1414,1415,1417,1418,1420,1421,1423,1424,1426,1427,1429,1430,1432,1433,1435,1436,1438,1439,1441,1442,1444,1445,1447,1448,1450,1451,1453,1454,1456,1457,1459,1460,1462,1463,1465,1466,1468,1469,1471,1472,1474,1475,1477,1478,1480,1481,1483,1484,1486,1487,1489,1490,1492,1493,1495,1496,1498,1499,1501,1502,1504,1505,1507,1508,1510,1511,1513,1514,1516,1517,1519,1520,1522,1523,1525,1526,1528,1529,1531,1532,1534,1535,1537,1538,1540,1541,1543,1544,1546,1547,1549,1550,1552,1553,1555,1556,1558,1559,1561,1562,1564,1565,1567,1568,1570,1571,1573,1574,1576,1577,1579,1580,1582,1583,1585,1586,1588,1589,1591,1592,1594,1595,1597,1598,1600,1601,1603,1604,1606,1607,1609,1610,1612,1613,1615,1616,1618,1619,1621,1622,1624,1625,1627,1628,1630,1631,1633,1634,1636,1637,1639,1640,1642,1643,1645,1646,1648,1649,1651,1652,1654,1655,1657,1658,1660,1661,1663,1664,1666,1667,1669,1670,1672,1673,1675,1676,1678,1679,1681,1682,1684,1685,1687,1688,1690,1691,1693,1694,1696,1697) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"HNSC (20531, 566)\n",
"gdac.broadinstitute.org_MESO.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 MESO\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"MESO (20531, 87)\n",
"gdac.broadinstitute.org_STAD.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 STAD\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512,514,515,517,518,520,521,523,524,526,527,529,530,532,533,535,536,538,539,541,542,544,545,547,548,550,551,553,554,556,557,559,560,562,563,565,566,568,569,571,572,574,575,577,578,580,581,583,584,586,587,589,590,592,593,595,596,598,599,601,602,604,605,607,608,610,611,613,614,616,617,619,620,622,623,625,626,628,629,631,632,634,635,637,638,640,641,643,644,646,647,649,650,652,653,655,656,658,659,661,662,664,665,667,668,670,671,673,674,676,677,679,680,682,683,685,686,688,689,691,692,694,695,697,698,700,701,703,704,706,707,709,710,712,713,715,716,718,719,721,722,724,725,727,728,730,731,733,734,736,737,739,740,742,743,745,746,748,749,751,752,754,755,757,758,760,761,763,764,766,767,769,770,772,773,775,776,778,779,781,782,784,785,787,788,790,791,793,794,796,797,799,800,802,803,805,806,808,809,811,812,814,815,817,818,820,821,823,824,826,827,829,830,832,833,835,836,838,839,841,842,844,845,847,848,850,851,853,854,856,857,859,860,862,863,865,866,868,869,871,872,874,875,877,878,880,881,883,884,886,887,889,890,892,893,895,896,898,899,901,902,904,905,907,908,910,911,913,914,916,917,919,920,922,923,925,926,928,929,931,932,934,935,937,938,940,941,943,944,946,947,949,950,952,953,955,956,958,959,961,962,964,965,967,968,970,971,973,974,976,977,979,980,982,983,985,986,988,989,991,992,994,995,997,998,1000,1001,1003,1004,1006,1007,1009,1010,1012,1013,1015,1016,1018,1019,1021,1022,1024,1025,1027,1028,1030,1031,1033,1034,1036,1037,1039,1040,1042,1043,1045,1046,1048,1049,1051,1052,1054,1055,1057,1058,1060,1061,1063,1064,1066,1067,1069,1070,1072,1073,1075,1076,1078,1079,1081,1082,1084,1085,1087,1088,1090,1091,1093,1094,1096,1097,1099,1100,1102,1103,1105,1106,1108,1109,1111,1112,1114,1115,1117,1118,1120,1121,1123,1124,1126,1127,1129,1130,1132,1133,1135,1136,1138,1139,1141,1142,1144,1145,1147,1148,1150,1151,1153,1154,1156,1157,1159,1160,1162,1163,1165,1166,1168,1169,1171,1172,1174,1175,1177,1178,1180,1181,1183,1184,1186,1187,1189,1190,1192,1193,1195,1196,1198,1199,1201,1202,1204,1205,1207,1208,1210,1211,1213,1214,1216,1217,1219,1220,1222,1223,1225,1226,1228,1229,1231,1232,1234,1235,1237,1238,1240,1241,1243,1244,1246,1247,1249,1250,1252,1253,1255,1256,1258,1259,1261,1262,1264,1265,1267,1268,1270,1271,1273,1274,1276,1277,1279,1280,1282,1283,1285,1286,1288,1289,1291,1292,1294,1295,1297,1298,1300,1301,1303,1304,1306,1307,1309,1310,1312,1313,1315,1316,1318,1319,1321,1322,1324,1325,1327,1328,1330,1331,1333,1334,1336,1337,1339,1340,1342,1343,1345,1346,1348,1349) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"STAD (20531, 450)\n",
"gdac.broadinstitute.org_OV.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 OV\n"
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"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512,514,515,517,518,520,521,523,524,526,527,529,530,532,533,535,536,538,539,541,542,544,545,547,548,550,551,553,554,556,557,559,560,562,563,565,566,568,569,571,572,574,575,577,578,580,581,583,584,586,587,589,590,592,593,595,596,598,599,601,602,604,605,607,608,610,611,613,614,616,617,619,620,622,623,625,626,628,629,631,632,634,635,637,638,640,641,643,644,646,647,649,650,652,653,655,656,658,659,661,662,664,665,667,668,670,671,673,674,676,677,679,680,682,683,685,686,688,689,691,692,694,695,697,698,700,701,703,704,706,707,709,710,712,713,715,716,718,719,721,722,724,725,727,728,730,731,733,734,736,737,739,740,742,743,745,746,748,749,751,752,754,755,757,758,760,761,763,764,766,767,769,770,772,773,775,776,778,779,781,782,784,785,787,788,790,791,793,794,796,797,799,800,802,803,805,806,808,809,811,812,814,815,817,818,820,821,823,824,826,827,829,830,832,833,835,836,838,839,841,842,844,845,847,848,850,851,853,854,856,857,859,860,862,863,865,866,868,869,871,872,874,875,877,878,880,881,883,884,886,887,889,890,892,893,895,896,898,899,901,902,904,905,907,908,910,911,913,914,916,917,919,920) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"OV (20531, 307)\n",
"gdac.broadinstitute.org_BLCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0 BLCA\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (1,2,4,5,7,8,10,11,13,14,16,17,19,20,22,23,25,26,28,29,31,32,34,35,37,38,40,41,43,44,46,47,49,50,52,53,55,56,58,59,61,62,64,65,67,68,70,71,73,74,76,77,79,80,82,83,85,86,88,89,91,92,94,95,97,98,100,101,103,104,106,107,109,110,112,113,115,116,118,119,121,122,124,125,127,128,130,131,133,134,136,137,139,140,142,143,145,146,148,149,151,152,154,155,157,158,160,161,163,164,166,167,169,170,172,173,175,176,178,179,181,182,184,185,187,188,190,191,193,194,196,197,199,200,202,203,205,206,208,209,211,212,214,215,217,218,220,221,223,224,226,227,229,230,232,233,235,236,238,239,241,242,244,245,247,248,250,251,253,254,256,257,259,260,262,263,265,266,268,269,271,272,274,275,277,278,280,281,283,284,286,287,289,290,292,293,295,296,298,299,301,302,304,305,307,308,310,311,313,314,316,317,319,320,322,323,325,326,328,329,331,332,334,335,337,338,340,341,343,344,346,347,349,350,352,353,355,356,358,359,361,362,364,365,367,368,370,371,373,374,376,377,379,380,382,383,385,386,388,389,391,392,394,395,397,398,400,401,403,404,406,407,409,410,412,413,415,416,418,419,421,422,424,425,427,428,430,431,433,434,436,437,439,440,442,443,445,446,448,449,451,452,454,455,457,458,460,461,463,464,466,467,469,470,472,473,475,476,478,479,481,482,484,485,487,488,490,491,493,494,496,497,499,500,502,503,505,506,508,509,511,512,514,515,517,518,520,521,523,524,526,527,529,530,532,533,535,536,538,539,541,542,544,545,547,548,550,551,553,554,556,557,559,560,562,563,565,566,568,569,571,572,574,575,577,578,580,581,583,584,586,587,589,590,592,593,595,596,598,599,601,602,604,605,607,608,610,611,613,614,616,617,619,620,622,623,625,626,628,629,631,632,634,635,637,638,640,641,643,644,646,647,649,650,652,653,655,656,658,659,661,662,664,665,667,668,670,671,673,674,676,677,679,680,682,683,685,686,688,689,691,692,694,695,697,698,700,701,703,704,706,707,709,710,712,713,715,716,718,719,721,722,724,725,727,728,730,731,733,734,736,737,739,740,742,743,745,746,748,749,751,752,754,755,757,758,760,761,763,764,766,767,769,770,772,773,775,776,778,779,781,782,784,785,787,788,790,791,793,794,796,797,799,800,802,803,805,806,808,809,811,812,814,815,817,818,820,821,823,824,826,827,829,830,832,833,835,836,838,839,841,842,844,845,847,848,850,851,853,854,856,857,859,860,862,863,865,866,868,869,871,872,874,875,877,878,880,881,883,884,886,887,889,890,892,893,895,896,898,899,901,902,904,905,907,908,910,911,913,914,916,917,919,920,922,923,925,926,928,929,931,932,934,935,937,938,940,941,943,944,946,947,949,950,952,953,955,956,958,959,961,962,964,965,967,968,970,971,973,974,976,977,979,980,982,983,985,986,988,989,991,992,994,995,997,998,1000,1001,1003,1004,1006,1007,1009,1010,1012,1013,1015,1016,1018,1019,1021,1022,1024,1025,1027,1028,1030,1031,1033,1034,1036,1037,1039,1040,1042,1043,1045,1046,1048,1049,1051,1052,1054,1055,1057,1058,1060,1061,1063,1064,1066,1067,1069,1070,1072,1073,1075,1076,1078,1079,1081,1082,1084,1085,1087,1088,1090,1091,1093,1094,1096,1097,1099,1100,1102,1103,1105,1106,1108,1109,1111,1112,1114,1115,1117,1118,1120,1121,1123,1124,1126,1127,1129,1130,1132,1133,1135,1136,1138,1139,1141,1142,1144,1145,1147,1148,1150,1151,1153,1154,1156,1157,1159,1160,1162,1163,1165,1166,1168,1169,1171,1172,1174,1175,1177,1178,1180,1181,1183,1184,1186,1187,1189,1190,1192,1193,1195,1196,1198,1199,1201,1202,1204,1205,1207,1208,1210,1211,1213,1214,1216,1217,1219,1220,1222,1223,1225,1226,1228,1229,1231,1232,1234,1235,1237,1238,1240,1241,1243,1244,1246,1247,1249,1250,1252,1253,1255,1256,1258,1259,1261,1262,1264,1265,1267,1268,1270,1271,1273,1274,1276,1277,1279,1280) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"BLCA (20531, 427)\n"
]
}
],
"source": [
"f_ext = \".rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.data.txt\"\n",
"for fpath in os.listdir(tcga_tmp_dir):\n",
" if fpath.startswith(\"gdac.broadinstitute.org\") and not fpath.endswith(\".tar.gz\") :\n",
" cohort = fpath.split(\"_\")[1].replace(\".Merge\",\"\")\n",
" #print(fpath, cohort)\n",
" fname = cohort + f_ext\n",
" try:\n",
" exprs = pd.read_csv(tcga_tmp_dir+\"/\"+fpath+\"/\"+fname,sep=\"\\t\",index_col=0)\n",
" # drop \"gene_id\" and keep only \"scaled_estimate\" columns\n",
" exprs = exprs.loc[:,exprs.T.loc[exprs.T[\"gene_id\"]==\"scaled_estimate\",:].index]\n",
" exprs = exprs.iloc[1:,]\n",
" exprs.rename(index = lambda x : int(x.split(\"|\")[1]),\n",
" columns = lambda x : x.replace(\".1\",\"\"),inplace = True)\n",
" exprs.index.name = \"ENTREZID\"\n",
" # convert scaled_extimates to log2(TPM+1)\n",
" exprs = exprs.applymap(lambda x : np.log2(float(x)*1000000+1))\n",
" exprs = exprs.sort_index()\n",
" exprs.to_csv(preprocessed_data_dir +\"TCGA-\"+cohort+\"_exprs.RSEMscaled_est2TPMplus1log2.tsv\",sep =\"\\t\")\n",
" print(cohort,exprs.shape)\n",
" except:\n",
" print(cohort,\"No expression data.\")\n",
"\n",
"\n",
" "
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
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" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>TCGA-2F-A9KO-01A-11R-A38B-07</th>\n",
" <th>TCGA-2F-A9KP-01A-11R-A38B-07</th>\n",
" <th>TCGA-2F-A9KQ-01A-11R-A38B-07</th>\n",
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" <th>TCGA-4Z-AA7N-01A-11R-A39I-07</th>\n",
" <th>TCGA-4Z-AA7O-01A-31R-A39I-07</th>\n",
" <th>TCGA-4Z-AA7Q-01A-11R-A39I-07</th>\n",
" <th>...</th>\n",
" <th>TCGA-ZF-AA4X-01A-11R-A38B-07</th>\n",
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" <th>TCGA-ZF-AA5N-01A-11R-A42T-07</th>\n",
" <th>TCGA-ZF-AA5P-01A-11R-A39I-07</th>\n",
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" <th>ENTREZID</th>\n",
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" <tr>\n",
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" <td>0.622532</td>\n",
" <td>0.837536</td>\n",
" <td>1.063692</td>\n",
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" <td>0.912991</td>\n",
" <td>1.612974</td>\n",
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" <td>0.870337</td>\n",
" <td>2.222218</td>\n",
" <td>...</td>\n",
" <td>1.523498</td>\n",
" <td>1.944983</td>\n",
" <td>2.372653</td>\n",
" <td>3.792826</td>\n",
" <td>3.479011</td>\n",
" <td>1.405645</td>\n",
" <td>1.572033</td>\n",
" <td>0.802134</td>\n",
" <td>0.420320</td>\n",
" <td>1.271811</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>8.034762</td>\n",
" <td>7.703466</td>\n",
" <td>7.782663</td>\n",
" <td>6.971443</td>\n",
" <td>6.047535</td>\n",
" <td>8.625286</td>\n",
" <td>6.235450</td>\n",
" <td>9.710621</td>\n",
" <td>7.270054</td>\n",
" <td>7.775153</td>\n",
" <td>...</td>\n",
" <td>5.611083</td>\n",
" <td>8.084193</td>\n",
" <td>10.095678</td>\n",
" <td>7.316936</td>\n",
" <td>8.761957</td>\n",
" <td>8.294718</td>\n",
" <td>7.737907</td>\n",
" <td>7.179355</td>\n",
" <td>4.904007</td>\n",
" <td>11.189585</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>2.167711</td>\n",
" <td>2.047625</td>\n",
" <td>2.951153</td>\n",
" <td>1.890493</td>\n",
" <td>1.988667</td>\n",
" <td>2.454169</td>\n",
" <td>2.643622</td>\n",
" <td>3.141316</td>\n",
" <td>2.077357</td>\n",
" <td>1.675782</td>\n",
" <td>...</td>\n",
" <td>3.949491</td>\n",
" <td>1.548279</td>\n",
" <td>3.722545</td>\n",
" <td>1.132057</td>\n",
" <td>2.568140</td>\n",
" <td>2.522893</td>\n",
" <td>1.725319</td>\n",
" <td>1.461496</td>\n",
" <td>1.847315</td>\n",
" <td>2.535479</td>\n",
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" <tr>\n",
" <th>10</th>\n",
" <td>0.000000</td>\n",
" <td>0.117556</td>\n",
" <td>0.000000</td>\n",
" <td>0.289701</td>\n",
" <td>0.000000</td>\n",
" <td>0.000000</td>\n",
" <td>0.000000</td>\n",
" <td>0.380386</td>\n",
" <td>0.056320</td>\n",
" <td>0.637087</td>\n",
" <td>...</td>\n",
" <td>0.505300</td>\n",
" <td>0.000000</td>\n",
" <td>0.138816</td>\n",
" <td>0.048032</td>\n",
" <td>0.048921</td>\n",
" <td>0.229931</td>\n",
" <td>0.000000</td>\n",
" <td>0.029659</td>\n",
" <td>0.000000</td>\n",
" <td>0.285390</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>2.467830</td>\n",
" <td>2.420112</td>\n",
" <td>0.644298</td>\n",
" <td>4.545485</td>\n",
" <td>0.052373</td>\n",
" <td>1.322490</td>\n",
" <td>0.434296</td>\n",
" <td>4.842291</td>\n",
" <td>0.000000</td>\n",
" <td>0.817122</td>\n",
" <td>...</td>\n",
" <td>0.551129</td>\n",
" <td>1.555709</td>\n",
" <td>3.774938</td>\n",
" <td>0.661099</td>\n",
" <td>3.624965</td>\n",
" <td>4.513976</td>\n",
" <td>4.705967</td>\n",
" <td>1.681905</td>\n",
" <td>3.356545</td>\n",
" <td>7.470335</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>1.607347</td>\n",
" <td>0.666421</td>\n",
" <td>2.125684</td>\n",
" <td>3.496252</td>\n",
" <td>0.287708</td>\n",
" <td>0.288064</td>\n",
" <td>0.244637</td>\n",
" <td>0.067852</td>\n",
" <td>7.387370</td>\n",
" <td>0.506860</td>\n",
" <td>...</td>\n",
" <td>1.877776</td>\n",
" <td>0.696837</td>\n",
" <td>0.000000</td>\n",
" <td>0.000000</td>\n",
" <td>0.186422</td>\n",
" <td>1.209302</td>\n",
" <td>0.000000</td>\n",
" <td>0.000000</td>\n",
" <td>0.000000</td>\n",
" <td>2.687331</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>6.712206</td>\n",
" <td>6.844482</td>\n",
" <td>6.394740</td>\n",
" <td>7.557387</td>\n",
" <td>6.178432</td>\n",
" <td>6.353666</td>\n",
" <td>6.690444</td>\n",
" <td>6.741365</td>\n",
" <td>7.059396</td>\n",
" <td>6.466467</td>\n",
" <td>...</td>\n",
" <td>6.842549</td>\n",
" <td>7.154221</td>\n",
" <td>6.930621</td>\n",
" <td>6.004271</td>\n",
" <td>7.079890</td>\n",
" <td>7.159629</td>\n",
" <td>7.005162</td>\n",
" <td>6.691151</td>\n",
" <td>7.000661</td>\n",
" <td>6.747745</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>0.080575</td>\n",
" <td>0.000000</td>\n",
" <td>0.211327</td>\n",
" <td>0.178252</td>\n",
" <td>0.086826</td>\n",
" <td>0.000000</td>\n",
" <td>0.085150</td>\n",
" <td>0.130796</td>\n",
" <td>0.000000</td>\n",
" <td>0.478062</td>\n",
" <td>...</td>\n",
" <td>0.000000</td>\n",
" <td>0.000000</td>\n",
" <td>0.000000</td>\n",
" <td>0.000000</td>\n",
" <td>0.147725</td>\n",
" <td>0.000000</td>\n",
" <td>0.221314</td>\n",
" <td>0.091143</td>\n",
" <td>0.000000</td>\n",
" <td>0.174953</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>6.763091</td>\n",
" <td>6.625150</td>\n",
" <td>6.082827</td>\n",
" <td>5.402623</td>\n",
" <td>5.592732</td>\n",
" <td>7.433563</td>\n",
" <td>5.714908</td>\n",
" <td>5.731613</td>\n",
" <td>5.883047</td>\n",
" <td>5.032016</td>\n",
" <td>...</td>\n",
" <td>5.766447</td>\n",
" <td>4.790307</td>\n",
" <td>5.707889</td>\n",
" <td>7.424335</td>\n",
" <td>8.709575</td>\n",
" <td>6.086463</td>\n",
" <td>6.234755</td>\n",
" <td>6.877003</td>\n",
" <td>5.877546</td>\n",
" <td>5.983488</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18</th>\n",
" <td>3.988948</td>\n",
" <td>4.263293</td>\n",
" <td>4.377654</td>\n",
" <td>2.923749</td>\n",
" <td>4.049974</td>\n",
" <td>1.382311</td>\n",
" <td>4.889327</td>\n",
" <td>3.960333</td>\n",
" <td>4.559524</td>\n",
" <td>0.999417</td>\n",
" <td>...</td>\n",
" <td>2.835719</td>\n",
" <td>1.746883</td>\n",
" <td>2.499375</td>\n",
" <td>0.784887</td>\n",
" <td>1.138534</td>\n",
" <td>3.009449</td>\n",
" <td>1.090132</td>\n",
" <td>0.552370</td>\n",
" <td>2.801317</td>\n",
" <td>1.614018</td>\n",
" </tr>\n",
" <tr>\n",
" <th>19</th>\n",
" <td>2.616904</td>\n",
" <td>1.357553</td>\n",
" <td>2.887098</td>\n",
" <td>2.551879</td>\n",
" <td>3.340053</td>\n",
" <td>4.326013</td>\n",
" <td>3.255879</td>\n",
" <td>3.513993</td>\n",
" <td>1.193602</td>\n",
" <td>3.132178</td>\n",
" <td>...</td>\n",
" <td>2.267587</td>\n",
" <td>2.991613</td>\n",
" <td>2.091500</td>\n",
" <td>3.461593</td>\n",
" <td>4.309989</td>\n",
" <td>3.239834</td>\n",
" <td>2.865977</td>\n",
" <td>3.039675</td>\n",
" <td>4.248400</td>\n",
" <td>2.405480</td>\n",
" </tr>\n",
" <tr>\n",
" <th>20</th>\n",
" <td>1.961844</td>\n",
" <td>3.090204</td>\n",
" <td>2.750104</td>\n",
" <td>2.616212</td>\n",
" <td>4.824872</td>\n",
" <td>1.875221</td>\n",
" <td>3.087467</td>\n",
" <td>3.481200</td>\n",
" <td>2.447453</td>\n",
" <td>1.753626</td>\n",
" <td>...</td>\n",
" <td>3.753183</td>\n",
" <td>3.149116</td>\n",
" <td>3.950087</td>\n",
" <td>1.512966</td>\n",
" <td>3.063315</td>\n",
" <td>2.664546</td>\n",
" <td>2.239061</td>\n",
" <td>2.201044</td>\n",
" <td>4.033922</td>\n",
" <td>2.951935</td>\n",
" </tr>\n",
" <tr>\n",
" <th>21</th>\n",
" <td>0.612701</td>\n",
" <td>2.171850</td>\n",
" <td>1.529668</td>\n",
" <td>0.874337</td>\n",
" <td>0.658170</td>\n",
" <td>3.151741</td>\n",
" <td>1.052042</td>\n",
" <td>2.201756</td>\n",
" <td>0.261264</td>\n",
" <td>1.009647</td>\n",
" <td>...</td>\n",
" <td>3.021527</td>\n",
" <td>1.113386</td>\n",
" <td>2.348143</td>\n",
" <td>0.415792</td>\n",
" <td>1.146891</td>\n",
" <td>0.973392</td>\n",
" <td>1.574075</td>\n",
" <td>0.609913</td>\n",
" <td>0.356479</td>\n",
" <td>3.029807</td>\n",
" </tr>\n",
" <tr>\n",
" <th>22</th>\n",
" <td>3.963608</td>\n",
" <td>3.558606</td>\n",
" <td>3.232821</td>\n",
" <td>4.034338</td>\n",
" <td>3.022397</td>\n",
" <td>2.919716</td>\n",
" <td>4.367590</td>\n",
" <td>3.606886</td>\n",
" <td>3.189884</td>\n",
" <td>3.521772</td>\n",
" <td>...</td>\n",
" <td>4.114507</td>\n",
" <td>3.389721</td>\n",
" <td>3.120593</td>\n",
" <td>3.509229</td>\n",
" <td>3.879658</td>\n",
" <td>3.396367</td>\n",
" <td>4.009166</td>\n",
" <td>3.136087</td>\n",
" <td>2.831521</td>\n",
" <td>3.356951</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23</th>\n",
" <td>5.866598</td>\n",
" <td>5.853114</td>\n",
" <td>5.628400</td>\n",
" <td>5.752864</td>\n",
" <td>5.695003</td>\n",
" <td>6.594964</td>\n",
" <td>6.738333</td>\n",
" <td>5.660017</td>\n",
" <td>5.480534</td>\n",
" <td>5.570752</td>\n",
" <td>...</td>\n",
" <td>6.430712</td>\n",
" <td>5.604658</td>\n",
" <td>5.590098</td>\n",
" <td>5.312926</td>\n",
" <td>6.285286</td>\n",
" <td>6.186670</td>\n",
" <td>6.549178</td>\n",
" <td>6.333991</td>\n",
" <td>5.442255</td>\n",
" <td>6.053878</td>\n",
" </tr>\n",
" <tr>\n",
" <th>24</th>\n",
" <td>1.926233</td>\n",
" <td>0.045424</td>\n",
" <td>0.055199</td>\n",
" <td>0.088273</td>\n",
" <td>0.064751</td>\n",
" <td>1.128087</td>\n",
" <td>0.803342</td>\n",
" <td>0.963160</td>\n",
" <td>0.533395</td>\n",
" <td>0.066792</td>\n",
" <td>...</td>\n",
" <td>1.379999</td>\n",
" <td>0.300011</td>\n",
" <td>0.421376</td>\n",
" <td>1.882620</td>\n",
" <td>0.130356</td>\n",
" <td>2.567049</td>\n",
" <td>2.568703</td>\n",
" <td>0.173096</td>\n",
" <td>0.388828</td>\n",
" <td>0.104554</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25</th>\n",
" <td>4.220049</td>\n",
" <td>4.463162</td>\n",
" <td>3.714227</td>\n",
" <td>4.611958</td>\n",
" <td>4.654495</td>\n",
" <td>4.446463</td>\n",
" <td>4.265416</td>\n",
" <td>5.059879</td>\n",
" <td>3.456701</td>\n",
" <td>3.441491</td>\n",
" <td>...</td>\n",
" <td>4.609126</td>\n",
" <td>3.930508</td>\n",
" <td>4.711956</td>\n",
" <td>4.138851</td>\n",
" <td>4.864261</td>\n",
" <td>4.814331</td>\n",
" <td>4.535544</td>\n",
" <td>4.680990</td>\n",
" <td>3.357347</td>\n",
" <td>5.748911</td>\n",
" </tr>\n",
" <tr>\n",
" <th>26</th>\n",
" <td>1.534503</td>\n",
" <td>0.457208</td>\n",
" <td>1.656747</td>\n",
" <td>3.666896</td>\n",
" <td>0.465448</td>\n",
" <td>0.336673</td>\n",
" <td>0.304059</td>\n",
" <td>0.574648</td>\n",
" <td>0.489768</td>\n",
" <td>0.309481</td>\n",
" <td>...</td>\n",
" <td>1.756336</td>\n",
" <td>0.761530</td>\n",
" <td>0.596701</td>\n",
" <td>1.438399</td>\n",
" <td>0.121543</td>\n",
" <td>1.735965</td>\n",
" <td>0.430035</td>\n",
" <td>0.857632</td>\n",
" <td>0.090871</td>\n",
" <td>0.192650</td>\n",
" </tr>\n",
" <tr>\n",
" <th>27</th>\n",
" <td>3.009672</td>\n",
" <td>2.538702</td>\n",
" <td>2.058677</td>\n",
" <td>2.333097</td>\n",
" <td>2.186895</td>\n",
" <td>3.246505</td>\n",
" <td>2.840525</td>\n",
" <td>3.008115</td>\n",
" <td>1.988889</td>\n",
" <td>1.045557</td>\n",
" <td>...</td>\n",
" <td>2.060089</td>\n",
" <td>1.888903</td>\n",
" <td>1.985187</td>\n",
" <td>2.370396</td>\n",
" <td>3.736276</td>\n",
" <td>1.990344</td>\n",
" <td>3.346693</td>\n",
" <td>4.048708</td>\n",
" <td>1.476133</td>\n",
" <td>2.492175</td>\n",
" </tr>\n",
" <tr>\n",
" <th>28</th>\n",
" <td>3.553466</td>\n",
" <td>0.071613</td>\n",
" <td>4.043810</td>\n",
" <td>1.998537</td>\n",
" <td>3.651975</td>\n",
" <td>0.970909</td>\n",
" <td>0.049227</td>\n",
" <td>2.933275</td>\n",
" <td>0.000000</td>\n",
" <td>4.048759</td>\n",
" <td>...</td>\n",
" <td>2.940057</td>\n",
" <td>0.047274</td>\n",
" <td>0.277321</td>\n",
" <td>0.241962</td>\n",
" <td>0.000000</td>\n",
" <td>2.330907</td>\n",
" <td>0.033785</td>\n",
" <td>0.052927</td>\n",
" <td>0.293858</td>\n",
" <td>0.617408</td>\n",
" </tr>\n",
" <tr>\n",
" <th>29</th>\n",
" <td>4.252114</td>\n",
" <td>5.314371</td>\n",
" <td>4.405773</td>\n",
" <td>4.809010</td>\n",
" <td>4.823228</td>\n",
" <td>3.875454</td>\n",
" <td>4.548557</td>\n",
" <td>5.491118</td>\n",
" <td>4.567789</td>\n",
" <td>5.541956</td>\n",
" <td>...</td>\n",
" <td>6.306159</td>\n",
" <td>5.983578</td>\n",
" <td>4.841091</td>\n",
" <td>3.985534</td>\n",
" <td>5.395005</td>\n",
" <td>5.227438</td>\n",
" <td>5.352269</td>\n",
" <td>6.153357</td>\n",
" <td>4.272364</td>\n",
" <td>4.636339</td>\n",
" </tr>\n",
" <tr>\n",
" <th>30</th>\n",
" <td>6.283626</td>\n",
" <td>7.041333</td>\n",
" <td>6.944863</td>\n",
" <td>6.671349</td>\n",
" <td>6.951327</td>\n",
" <td>5.968195</td>\n",
" <td>6.568039</td>\n",
" <td>6.418584</td>\n",
" <td>6.085184</td>\n",
" <td>5.676482</td>\n",
" <td>...</td>\n",
" <td>7.011171</td>\n",
" <td>6.898103</td>\n",
" <td>6.407046</td>\n",
" <td>6.627765</td>\n",
" <td>4.923261</td>\n",
" <td>6.389457</td>\n",
" <td>6.324138</td>\n",
" <td>5.236563</td>\n",
" <td>6.822422</td>\n",
" <td>6.143988</td>\n",
" </tr>\n",
" <tr>\n",
" <th>31</th>\n",
" <td>4.650181</td>\n",
" <td>4.974986</td>\n",
" <td>4.473319</td>\n",
" <td>5.608256</td>\n",
" <td>5.003486</td>\n",
" <td>4.237128</td>\n",
" <td>4.899172</td>\n",
" <td>4.801196</td>\n",
" <td>4.411286</td>\n",
" <td>4.604509</td>\n",
" <td>...</td>\n",
" <td>5.489832</td>\n",
" <td>4.361208</td>\n",
" <td>4.499776</td>\n",
" <td>4.099796</td>\n",
" <td>4.310456</td>\n",
" <td>5.287507</td>\n",
" <td>3.789480</td>\n",
" <td>4.593572</td>\n",
" <td>4.810476</td>\n",
" <td>4.482980</td>\n",
" </tr>\n",
" <tr>\n",
" <th>32</th>\n",
" <td>1.287524</td>\n",
" <td>0.505654</td>\n",
" <td>0.763694</td>\n",
" <td>1.874325</td>\n",
" <td>0.733106</td>\n",
" <td>0.757118</td>\n",
" <td>1.871018</td>\n",
" <td>2.696572</td>\n",
" <td>0.690042</td>\n",
" <td>2.033386</td>\n",
" <td>...</td>\n",
" <td>2.531524</td>\n",
" <td>1.201789</td>\n",
" <td>2.071635</td>\n",
" <td>0.923636</td>\n",
" <td>1.525026</td>\n",
" <td>1.321938</td>\n",
" <td>1.662648</td>\n",
" <td>1.231275</td>\n",
" <td>0.364992</td>\n",
" <td>3.270376</td>\n",
" </tr>\n",
" <tr>\n",
" <th>33</th>\n",
" <td>0.407168</td>\n",
" <td>0.272536</td>\n",
" <td>0.191193</td>\n",
" <td>0.570630</td>\n",
" <td>0.159784</td>\n",
" <td>0.000000</td>\n",
" <td>0.401075</td>\n",
" <td>0.162440</td>\n",
" <td>0.000000</td>\n",
" <td>0.365014</td>\n",
" <td>...</td>\n",
" <td>2.082781</td>\n",
" <td>0.051872</td>\n",
" <td>0.023798</td>\n",
" <td>0.070492</td>\n",
" <td>0.118533</td>\n",
" <td>0.513203</td>\n",
" <td>0.000000</td>\n",
" <td>0.269587</td>\n",
" <td>0.000000</td>\n",
" <td>0.264252</td>\n",
" </tr>\n",
" <tr>\n",
" <th>34</th>\n",
" <td>4.699257</td>\n",
" <td>5.466270</td>\n",
" <td>5.665893</td>\n",
" <td>5.476256</td>\n",
" <td>3.955474</td>\n",
" <td>4.042493</td>\n",
" <td>5.060120</td>\n",
" <td>5.352350</td>\n",
" <td>4.347544</td>\n",
" <td>4.789519</td>\n",
" <td>...</td>\n",
" <td>6.376422</td>\n",
" <td>4.577791</td>\n",
" <td>3.492034</td>\n",
" <td>4.605242</td>\n",
" <td>4.283358</td>\n",
" <td>4.977100</td>\n",
" <td>4.716416</td>\n",
" <td>4.580350</td>\n",
" <td>3.954026</td>\n",
" <td>4.304655</td>\n",
" </tr>\n",
" <tr>\n",
" <th>35</th>\n",
" <td>4.221315</td>\n",
" <td>4.060692</td>\n",
" <td>5.565621</td>\n",
" <td>4.414742</td>\n",
" <td>4.286086</td>\n",
" <td>4.366536</td>\n",
" <td>4.255144</td>\n",
" <td>3.561433</td>\n",
" <td>3.889248</td>\n",
" <td>4.366157</td>\n",
" <td>...</td>\n",
" <td>4.455009</td>\n",
" <td>4.415570</td>\n",
" <td>4.746772</td>\n",
" <td>4.056638</td>\n",
" <td>3.347017</td>\n",
" <td>4.584887</td>\n",
" <td>3.579932</td>\n",
" <td>3.506765</td>\n",
" <td>4.248824</td>\n",
" <td>5.511854</td>\n",
" </tr>\n",
" <tr>\n",
" <th>36</th>\n",
" <td>2.546490</td>\n",
" <td>4.141481</td>\n",
" <td>4.002538</td>\n",
" <td>2.430160</td>\n",
" <td>2.272737</td>\n",
" <td>2.416162</td>\n",
" <td>3.025325</td>\n",
" <td>3.605907</td>\n",
" <td>3.095087</td>\n",
" <td>1.872858</td>\n",
" <td>...</td>\n",
" <td>2.938874</td>\n",
" <td>1.959830</td>\n",
" <td>1.615353</td>\n",
" <td>0.780055</td>\n",
" <td>2.305503</td>\n",
" <td>3.151896</td>\n",
" <td>1.116940</td>\n",
" <td>1.183204</td>\n",
" <td>1.778956</td>\n",
" <td>2.279470</td>\n",
" </tr>\n",
" <tr>\n",
" <th>37</th>\n",
" <td>8.221469</td>\n",
" <td>8.484431</td>\n",
" <td>8.220426</td>\n",
" <td>7.658984</td>\n",
" <td>7.298956</td>\n",
" <td>7.522056</td>\n",
" <td>7.826961</td>\n",
" <td>7.369623</td>\n",
" <td>8.441356</td>\n",
" <td>7.439627</td>\n",
" <td>...</td>\n",
" <td>8.781912</td>\n",
" <td>8.247836</td>\n",
" <td>8.192882</td>\n",
" <td>7.438942</td>\n",
" <td>7.362950</td>\n",
" <td>7.659910</td>\n",
" <td>7.255310</td>\n",
" <td>7.487467</td>\n",
" <td>8.403723</td>\n",
" <td>7.616378</td>\n",
" </tr>\n",
" <tr>\n",
" <th>38</th>\n",
" <td>4.277477</td>\n",
" <td>4.804687</td>\n",
" <td>4.168925</td>\n",
" <td>2.910270</td>\n",
" <td>3.432268</td>\n",
" <td>4.960705</td>\n",
" <td>4.294950</td>\n",
" <td>4.475646</td>\n",
" <td>2.691840</td>\n",
" <td>3.959515</td>\n",
" <td>...</td>\n",
" <td>4.490428</td>\n",
" <td>4.263302</td>\n",
" <td>4.684854</td>\n",
" <td>4.018424</td>\n",
" <td>5.138271</td>\n",
" <td>4.254429</td>\n",
" <td>4.615857</td>\n",
" <td>3.647883</td>\n",
" <td>4.821318</td>\n",
" <td>5.106815</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>100271722</th>\n",
" <td>1.381865</td>\n",
" <td>0.559305</td>\n",
" <td>2.507135</td>\n",
" <td>2.419759</td>\n",
" <td>2.330566</td>\n",
" <td>0.527452</td>\n",
" <td>1.290149</td>\n",
" <td>1.200610</td>\n",
" <td>1.584978</td>\n",
" <td>0.413451</td>\n",
" <td>...</td>\n",
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"</table>\n",
"<p>20531 rows × 427 columns</p>\n",
"</div>"
],
"text/plain": [
" TCGA-2F-A9KO-01A-11R-A38B-07 TCGA-2F-A9KP-01A-11R-A38B-07 \\\n",
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"... ... ... \n",
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" TCGA-4Z-AA7M-01A-11R-A39I-07 TCGA-4Z-AA7N-01A-11R-A39I-07 \\\n",
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"... ... ... \n",
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"... ... ... \n",
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"... ... ... \n",
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"\n",
" TCGA-ZF-AA51-01A-21R-A39I-07 TCGA-ZF-AA52-01A-12R-A39I-07 \\\n",
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"... ... ... \n",
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"\n",
" TCGA-ZF-AA53-01A-11R-A39I-07 TCGA-ZF-AA54-01A-11R-A39I-07 \\\n",
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"... ... ... \n",
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"\n",
" TCGA-ZF-AA56-01A-31R-A39I-07 TCGA-ZF-AA58-01A-12R-A42T-07 \\\n",
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"... ... ... \n",
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"\n",
" TCGA-ZF-AA5H-01A-11R-A39I-07 TCGA-ZF-AA5N-01A-11R-A42T-07 \\\n",
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"... ... ... \n",
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"\n",
" TCGA-ZF-AA5P-01A-11R-A39I-07 \n",
"ENTREZID \n",
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"... ... \n",
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"\n",
"[20531 rows x 427 columns]"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"exprs"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
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Datasets
Models
