2281 lines (2280 with data), 177.7 kB
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"suppressPackageStartupMessages(library(\"affy\"))\n",
"suppressPackageStartupMessages(library(\"affyio\"))\n",
"\n",
"\n",
"################################ functions ##########################################\n",
"\n",
"# download and install BrainArray files \n",
"\n",
"getBrainArrayFile <- function(chipname,what,version=\"22.0.0\",gene_id_type=\"ensg\", download_dir=getwd()){\n",
" fname <- paste0(chipname,gene_id_type,what,\"_\",version,\".tar.gz\")\n",
" link <- paste0(\"http://mbni.org/customcdf/\",version,\"/\",gene_id_type,\".download/\",fname)\n",
" #print(link)\n",
" fpath <- paste0(download_dir,fname)\n",
" download.file(link, destfile = fpath, method = \"wget\")\n",
" suppressWarnings(install.packages(fpath, repos = NULL, type=\"source\"))\n",
" libname <- paste0(chipname,gene_id_type,what)\n",
" suppressPackageStartupMessages(library(libname,character.only = T))\n",
" return(libname)\n",
"}\n",
"# for Ensembl:\n",
"# entrezg -> ensg\n",
"# .db -> probe\n",
"installBrainArrayCDFandDB <- function(chipname,version=\"22.0.0\",gene_id_type=\"entrezg\", download_dir=getwd()){\n",
" customCDFname <- getBrainArrayFile(chipname,\"cdf\",version=version,\n",
" gene_id_type=gene_id_type, download_dir=download_dir)\n",
" # the same way for probe file\n",
" \n",
" customDBname <- getBrainArrayFile(chipname,\".db\",version=version,\n",
" gene_id_type=gene_id_type, download_dir=download_dir)\n",
" return (list(customCDFname=customCDFname, customDBname = customDBname))\n",
"}\n",
"\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# The effect of CDF and annotation on the results of affy:justRMA()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Threre are two crucial reference files required to preprocess raw microarray data, i.e. to get gene expression profiels from .CEL files:\n",
"\n",
"* CDF file (or more precisely the environment generated from the source file) defines how probes unitied into probesets and stores probe location to probeset mapping. In Affymetrix microarrays each probeset includes ~10-20 oligonucleotide probes. Some of them are not specific enough or designed for QC (starting with \"AFFX\") and therefore are not suitable for gene expression estimation. Different CDFs edfine sligtly different mapping with completely different probe names. \n",
"\n",
"Options:\n",
" - AnnotationDbi. By default affy imports CDF environments from http://master.bioconductor.org/packages/release/data/annotation/.\n",
" - BrainArray provides updated probeset definition (current v22.0.0, Jun 21, 2017) correponding to the latest genome and transcriptome assemblies, when Affymetrix definition may be outdated. The impact of CDF on the result of differential expression analysis may be high:\n",
" https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.20433\n",
" https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-48\n",
"\n",
"\n",
"* Annotation file of DB contains probeset IDs mapping to gene or transcript IDs. Since for some genes more than one probeset exist, per gene expression is computed as an average over probesets belonging to the same gene.\n",
"Options:\n",
" - AnnotationDbi - annotation is missing for HuGene-1_0-st-v1 platform.\n",
" - BrainArray DB - covers approximately 100 unique genes momre than AnnotationDbi\n",
" - biomaRt - allows to select a specific Ensemble version, e.g. 37.75. Ensemble describes their own pipeline of probe-to-gene mapping https://uswest.ensembl.org/info/genome/microarray_probe_set_mapping.html. No annotation for HGU-219 platform. \n",
" \n",
"### Selection of gene nomenclature\n",
"Options:\n",
" - HGNC gene Symbols\n",
" + human-readble\n",
" - not stable; IL8 can be changed to CXCL8; ~10% of IDs from PDX do not map on the current HGNC. \n",
" + despite that, in many studies gene symbols are the only IDs reported. PDX reports only gene symbols in expression and CNA data tables. \n",
" - many IDs do not correspond to genes but to loci associated with a phenotype; this is very cofusing for transcriptomics. At the same time, many RNAs and pseudogenes are not presented in this nomenclature. \n",
" - Entrez IDs\n",
" + numeric gene IDs, seem to be more stable\n",
" - not human-readable\n",
" \n",
" - ENSEMBL IDs\n",
" + these ids correspond to a certain transcriptome assembly, so there are no loci and there are non-coding RNA\n",
" - BrainArray and AnnotationDbi mappings to Ensemble mixing up ENSEMBL IDs from Grch37 and Grch38, athough here https://www.sciencedirect.com/science/article/pii/S1535610817302532 BrainArray CDF was used together with transcriptome annotation \n",
" \n",
"# Conclusions\n",
"in the current version we use: \n",
" - the latest CDF from BrainArray \n",
"and \n",
" - BrainArray annotation to map probesets to Entrez gene IDs, since they are more stable than HGNC. \n",
" \n",
"In general, for transcriptomic and proteomic studies Ensembl nomencalture would be more appropriate, because it covers more transcripts, do not include \"phenotype only\" loci and allows to control assembe versions. However, both BrainArray and AnnotationDbi some microarray probes mapped to multiple Ensembl IDs due to mixing up 37th and 38th assmblies. \n",
"BiomaRt developed by Ensembl would be an alternative soution, but GDSC, a key dataset for our study, is profiled by affymetrix HGU-219 platform, absent in biomaRt. \n",
"\n",
"\n",
"# To Do:\n",
"- try RMA vs gcRMA vs MAS5 normalizations\n",
"- perform QC "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Statistics of gene annotations in BrainArray\n",
"\"hgu219hs\",\"hgu133plus2hs\",\"hgu95av2hs\",\"hgu133ahs\",\"hgu133bhs\",\"hugene10sths\"\n"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"hgu219hs ENTREZ 18646 ENSEMBL 20342 ENSEMBL dups 20757 SYMBOL 18646 \n",
"hgu133plus2hs ENTREZ 20343 ENSEMBL 20928 ENSEMBL dups 22473 SYMBOL 20343 \n",
"hgu95av2hs ENTREZ 8450 ENSEMBL 9443 ENSEMBL dups 9554 SYMBOL 8450 \n",
"hgu133ahs ENTREZ 12250 ENSEMBL 13538 ENSEMBL dups 13842 SYMBOL 12250 \n",
"hgu133bhs ENTREZ 9074 ENSEMBL 8887 ENSEMBL dups 9671 SYMBOL 9074 \n",
"hugene10sths ENTREZ 20663 ENSEMBL 21371 ENSEMBL dups 22943 SYMBOL 20663 \n"
]
}
],
"source": [
"# how many unique gene ids in each annotation\n",
"for (platform in c(\"hgu219hs\",\"hgu133plus2hs\",\"hgu95av2hs\",\"hgu133ahs\",\"hgu133bhs\",\"hugene10sths\")){\n",
" customAnno <- installBrainArrayCDFandDB(platform,version='22.0.0',gene_id_type=\"entrezg\",\n",
" download_dir=\"/home/olya/SFU/Hossein/arrays/\")\n",
" anno_ENTR <- suppressMessages(select(get(customAnno$customDBname), keytype=\"PROBEID\", \n",
" columns=c(\"ENTREZID\"), keys=keys(get(customAnno$customDBname))))\n",
" anno_ENS <- suppressMessages(select(get(customAnno$customDBname), keytype=\"PROBEID\", \n",
" columns=c(\"ENSEMBL\"), keys=keys(get(customAnno$customDBname))))\n",
" anno_SYM <- suppressMessages(select(get(customAnno$customDBname), keytype=\"PROBEID\", \n",
" columns=c(\"SYMBOL\"), keys=keys(get(customAnno$customDBname))))\n",
" cat(paste(platform,\"ENTREZ\",length(unique(anno_ENTR$ENTREZID)),\n",
" \"ENSEMBL\",length(unique(anno_ENS$ENSEMBL)),\"ENSEMBL dups\",\n",
" length(duplicated(anno_ENS$PROBEID)),\n",
" \"SYMBOL\",length(unique(anno_SYM$SYMBOL)),\"\\n\",sep=\" \"))\n",
" \n",
"}"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Here we show, that our microarray preprocessing pipeline produces almost the same results as in He et al. 2018:\n",
"https://academic.oup.com/bioinformatics/article/34/16/2808/4924716\n",
"by Xiao He, Lukas Folkman and Karsten Borgwardt \n",
"\n",
"For that we preprocess raw expression data from GDSC and GSE (docetaxel clinica trials) and compare it with expression profiles provided by Lukas Folkman\n",
"\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Preprocess raw GDSC data from E-MTAB-3610 with BrainArray CDF and DB\n",
" * get platform names from CEL headers\n",
" * download and install corresponding BrainArray CDF and DB\n",
" * read full CEL files affy::justRMA() with specified cdfname ( hus we replace the default CDF with custom CDF from BrainArray); justRMA sumarizes CEL intensities according to provided CDF, bg-corrects, RMA-normalizes and log2-transforms. \n",
" \n",
" [docs. : \"cdfname If set to NULL, then the usual cdf package based on Affymetrix' mappings will be used.\"]\n",
" According to affy manual, default CDF are taken from here: http://bioconductor.org/help/bioc-views/release/data/annotation/ (and most of them are AnnotationDbi packages)\n",
" \n"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"1018"
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"text/latex": [
"1018"
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"text/markdown": [
"1018"
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"[1] 1018"
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},
"metadata": {},
"output_type": "display_data"
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{
"data": {
"text/html": [
"'hgu219cdf'"
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"text/latex": [
"'hgu219cdf'"
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"'hgu219cdf'"
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"[1] \"hgu219cdf\""
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"source": [
"cel_file_dir = \"arrays/E-MTAB-3610/\"\n",
"getSnames <- function(sname,ext=\".cel\"){\n",
" sname <- sub(ext, \"\", sname)\n",
" sname <- unlist(sname)[1]\n",
" return(sname)\n",
"}\n",
"fnames <- list.files(cel_file_dir ,pattern = \".cel\")\n",
"snames <- lapply(fnames, getSnames)\n",
"snames <- unlist(snames)\n",
"# number of CEL files:\n",
"length(snames)\n",
"#get CDF names from platform names from CEL headers \n",
"getCDFname <- function(fname,dir=getwd()){\n",
" cel_header <-affyio::read.celfile.header(paste0(dir,fname))\n",
" return(cleancdfname(cel_header$cdfName))\n",
"}\n",
"cdf_basenames <- unique(unlist(lapply(fnames,getCDFname, dir=cel_file_dir)))\n",
"cdf_basenames \n",
"# add processing of batches in future\n",
"cdf_basename <- sub(\"cdf\",\"\",cdf_basenames[1])\n",
"\n",
"# load BrainArray\n",
"customAnno <- installBrainArrayCDFandDB(paste0(cdf_basename,\"hs\"),version='22.0.0',gene_id_type=\"entrezg\",\n",
" download_dir=\"/home/olya/SFU/Hossein/arrays/\")\n",
"#customAnno"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"ExpressionSet (storageMode: lockedEnvironment)\n",
"assayData: 18653 features, 1018 samples \n",
" element names: exprs, se.exprs \n",
"protocolData\n",
" sampleNames: 5500994157493061613625_A01 5500994157493061613625_A02\n",
" ... 5500994175999120813240_H11 (1018 total)\n",
" varLabels: ScanDate\n",
" varMetadata: labelDescription\n",
"phenoData\n",
" sampleNames: 5500994157493061613625_A01 5500994157493061613625_A02\n",
" ... 5500994175999120813240_H11 (1018 total)\n",
" varLabels: sample\n",
" varMetadata: labelDescription\n",
"featureData: none\n",
"experimentData: use 'experimentData(object)'\n",
"Annotation: hgu219hsentrezgcdf "
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th></th><th scope=col>5500994157493061613625_A01</th><th scope=col>5500994157493061613625_A02</th><th scope=col>5500994157493061613625_A03</th><th scope=col>5500994157493061613625_A04</th><th scope=col>5500994157493061613625_A05</th><th scope=col>5500994157493061613625_A06</th><th scope=col>5500994157493061613625_A07</th><th scope=col>5500994157493061613625_A08</th><th scope=col>5500994157493061613625_A09</th><th scope=col>5500994157493061613625_A10</th><th scope=col>⋯</th><th scope=col>5500994175999120813240_H02</th><th scope=col>5500994175999120813240_H03</th><th scope=col>5500994175999120813240_H04</th><th scope=col>5500994175999120813240_H05</th><th scope=col>5500994175999120813240_H06</th><th scope=col>5500994175999120813240_H07</th><th scope=col>5500994175999120813240_H08</th><th scope=col>5500994175999120813240_H09</th><th scope=col>5500994175999120813240_H10</th><th scope=col>5500994175999120813240_H11</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><th scope=row>1_at</th><td>6.210671 </td><td>5.029226 </td><td>5.513632 </td><td>4.208249 </td><td>3.402282 </td><td>4.914035 </td><td>3.827411 </td><td>5.147878 </td><td>3.110751 </td><td>5.054884 </td><td>⋯ </td><td>4.273165 </td><td>3.442682 </td><td> 4.923977</td><td>2.901377 </td><td>4.528475 </td><td>5.079415 </td><td>2.959578 </td><td>3.094308 </td><td>4.045297 </td><td>5.339831 </td></tr>\n",
"\t<tr><th scope=row>10_at</th><td>3.091616 </td><td>2.925953 </td><td>3.186898 </td><td>3.090349 </td><td>5.070067 </td><td>2.912126 </td><td>3.028838 </td><td>3.049457 </td><td>2.996803 </td><td>3.487389 </td><td>⋯ </td><td>3.169651 </td><td>3.094766 </td><td> 2.978914</td><td>3.312476 </td><td>3.271839 </td><td>3.004895 </td><td>3.039933 </td><td>3.346097 </td><td>3.049132 </td><td>3.238387 </td></tr>\n",
"\t<tr><th scope=row>100_at</th><td>8.956673 </td><td>7.687656 </td><td>7.944700 </td><td>9.259829 </td><td>7.017582 </td><td>6.905274 </td><td>9.751193 </td><td>7.540148 </td><td>5.773222 </td><td>3.324055 </td><td>⋯ </td><td>6.993797 </td><td>8.793967 </td><td>11.941098</td><td>9.371423 </td><td>7.939735 </td><td>9.046963 </td><td>6.055670 </td><td>7.746151 </td><td>6.814890 </td><td>5.698509 </td></tr>\n",
"\t<tr><th scope=row>1000_at</th><td>7.613752 </td><td>3.066216 </td><td>6.634775 </td><td>8.708245 </td><td>8.754138 </td><td>6.827789 </td><td>3.282731 </td><td>8.739057 </td><td>9.572730 </td><td>3.037323 </td><td>⋯ </td><td>3.816762 </td><td>3.022264 </td><td> 5.862574</td><td>6.649221 </td><td>8.565891 </td><td>6.079522 </td><td>4.536474 </td><td>4.141976 </td><td>8.703439 </td><td>4.722706 </td></tr>\n",
"\t<tr><th scope=row>10000_at</th><td>5.836163 </td><td>4.045650 </td><td>2.832221 </td><td>4.290599 </td><td>4.776181 </td><td>4.715363 </td><td>3.575370 </td><td>4.213761 </td><td>5.838059 </td><td>2.894429 </td><td>⋯ </td><td>5.388321 </td><td>2.827153 </td><td> 3.599740</td><td>5.266808 </td><td>3.960827 </td><td>5.060720 </td><td>5.723751 </td><td>3.494836 </td><td>3.297643 </td><td>5.769323 </td></tr>\n",
"\t<tr><th scope=row>10001_at</th><td>6.927791 </td><td>7.396852 </td><td>7.097197 </td><td>7.389636 </td><td>8.015398 </td><td>7.107112 </td><td>7.659327 </td><td>6.855786 </td><td>7.808900 </td><td>7.290094 </td><td>⋯ </td><td>7.876365 </td><td>8.314665 </td><td> 8.197616</td><td>7.431327 </td><td>8.092348 </td><td>6.973491 </td><td>8.852970 </td><td>8.436557 </td><td>7.824003 </td><td>7.584112 </td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|llllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllll}\n",
" & 5500994157493061613625\\_A01 & 5500994157493061613625\\_A02 & 5500994157493061613625\\_A03 & 5500994157493061613625\\_A04 & 5500994157493061613625\\_A05 & 5500994157493061613625\\_A06 & 5500994157493061613625\\_A07 & 5500994157493061613625\\_A08 & 5500994157493061613625\\_A09 & 5500994157493061613625\\_A10 & ⋯ & 5500994175999120813240\\_H02 & 5500994175999120813240\\_H03 & 5500994175999120813240\\_H04 & 5500994175999120813240\\_H05 & 5500994175999120813240\\_H06 & 5500994175999120813240\\_H07 & 5500994175999120813240\\_H08 & 5500994175999120813240\\_H09 & 5500994175999120813240\\_H10 & 5500994175999120813240\\_H11\\\\\n",
"\\hline\n",
"\t1\\_at & 6.210671 & 5.029226 & 5.513632 & 4.208249 & 3.402282 & 4.914035 & 3.827411 & 5.147878 & 3.110751 & 5.054884 & ⋯ & 4.273165 & 3.442682 & 4.923977 & 2.901377 & 4.528475 & 5.079415 & 2.959578 & 3.094308 & 4.045297 & 5.339831 \\\\\n",
"\t10\\_at & 3.091616 & 2.925953 & 3.186898 & 3.090349 & 5.070067 & 2.912126 & 3.028838 & 3.049457 & 2.996803 & 3.487389 & ⋯ & 3.169651 & 3.094766 & 2.978914 & 3.312476 & 3.271839 & 3.004895 & 3.039933 & 3.346097 & 3.049132 & 3.238387 \\\\\n",
"\t100\\_at & 8.956673 & 7.687656 & 7.944700 & 9.259829 & 7.017582 & 6.905274 & 9.751193 & 7.540148 & 5.773222 & 3.324055 & ⋯ & 6.993797 & 8.793967 & 11.941098 & 9.371423 & 7.939735 & 9.046963 & 6.055670 & 7.746151 & 6.814890 & 5.698509 \\\\\n",
"\t1000\\_at & 7.613752 & 3.066216 & 6.634775 & 8.708245 & 8.754138 & 6.827789 & 3.282731 & 8.739057 & 9.572730 & 3.037323 & ⋯ & 3.816762 & 3.022264 & 5.862574 & 6.649221 & 8.565891 & 6.079522 & 4.536474 & 4.141976 & 8.703439 & 4.722706 \\\\\n",
"\t10000\\_at & 5.836163 & 4.045650 & 2.832221 & 4.290599 & 4.776181 & 4.715363 & 3.575370 & 4.213761 & 5.838059 & 2.894429 & ⋯ & 5.388321 & 2.827153 & 3.599740 & 5.266808 & 3.960827 & 5.060720 & 5.723751 & 3.494836 & 3.297643 & 5.769323 \\\\\n",
"\t10001\\_at & 6.927791 & 7.396852 & 7.097197 & 7.389636 & 8.015398 & 7.107112 & 7.659327 & 6.855786 & 7.808900 & 7.290094 & ⋯ & 7.876365 & 8.314665 & 8.197616 & 7.431327 & 8.092348 & 6.973491 & 8.852970 & 8.436557 & 7.824003 & 7.584112 \\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"| <!--/--> | 5500994157493061613625_A01 | 5500994157493061613625_A02 | 5500994157493061613625_A03 | 5500994157493061613625_A04 | 5500994157493061613625_A05 | 5500994157493061613625_A06 | 5500994157493061613625_A07 | 5500994157493061613625_A08 | 5500994157493061613625_A09 | 5500994157493061613625_A10 | ⋯ | 5500994175999120813240_H02 | 5500994175999120813240_H03 | 5500994175999120813240_H04 | 5500994175999120813240_H05 | 5500994175999120813240_H06 | 5500994175999120813240_H07 | 5500994175999120813240_H08 | 5500994175999120813240_H09 | 5500994175999120813240_H10 | 5500994175999120813240_H11 | \n",
"|---|---|---|---|---|---|\n",
"| 1_at | 6.210671 | 5.029226 | 5.513632 | 4.208249 | 3.402282 | 4.914035 | 3.827411 | 5.147878 | 3.110751 | 5.054884 | ⋯ | 4.273165 | 3.442682 | 4.923977 | 2.901377 | 4.528475 | 5.079415 | 2.959578 | 3.094308 | 4.045297 | 5.339831 | \n",
"| 10_at | 3.091616 | 2.925953 | 3.186898 | 3.090349 | 5.070067 | 2.912126 | 3.028838 | 3.049457 | 2.996803 | 3.487389 | ⋯ | 3.169651 | 3.094766 | 2.978914 | 3.312476 | 3.271839 | 3.004895 | 3.039933 | 3.346097 | 3.049132 | 3.238387 | \n",
"| 100_at | 8.956673 | 7.687656 | 7.944700 | 9.259829 | 7.017582 | 6.905274 | 9.751193 | 7.540148 | 5.773222 | 3.324055 | ⋯ | 6.993797 | 8.793967 | 11.941098 | 9.371423 | 7.939735 | 9.046963 | 6.055670 | 7.746151 | 6.814890 | 5.698509 | \n",
"| 1000_at | 7.613752 | 3.066216 | 6.634775 | 8.708245 | 8.754138 | 6.827789 | 3.282731 | 8.739057 | 9.572730 | 3.037323 | ⋯ | 3.816762 | 3.022264 | 5.862574 | 6.649221 | 8.565891 | 6.079522 | 4.536474 | 4.141976 | 8.703439 | 4.722706 | \n",
"| 10000_at | 5.836163 | 4.045650 | 2.832221 | 4.290599 | 4.776181 | 4.715363 | 3.575370 | 4.213761 | 5.838059 | 2.894429 | ⋯ | 5.388321 | 2.827153 | 3.599740 | 5.266808 | 3.960827 | 5.060720 | 5.723751 | 3.494836 | 3.297643 | 5.769323 | \n",
"| 10001_at | 6.927791 | 7.396852 | 7.097197 | 7.389636 | 8.015398 | 7.107112 | 7.659327 | 6.855786 | 7.808900 | 7.290094 | ⋯ | 7.876365 | 8.314665 | 8.197616 | 7.431327 | 8.092348 | 6.973491 | 8.852970 | 8.436557 | 7.824003 | 7.584112 | \n",
"\n",
"\n"
],
"text/plain": [
" 5500994157493061613625_A01 5500994157493061613625_A02\n",
"1_at 6.210671 5.029226 \n",
"10_at 3.091616 2.925953 \n",
"100_at 8.956673 7.687656 \n",
"1000_at 7.613752 3.066216 \n",
"10000_at 5.836163 4.045650 \n",
"10001_at 6.927791 7.396852 \n",
" 5500994157493061613625_A03 5500994157493061613625_A04\n",
"1_at 5.513632 4.208249 \n",
"10_at 3.186898 3.090349 \n",
"100_at 7.944700 9.259829 \n",
"1000_at 6.634775 8.708245 \n",
"10000_at 2.832221 4.290599 \n",
"10001_at 7.097197 7.389636 \n",
" 5500994157493061613625_A05 5500994157493061613625_A06\n",
"1_at 3.402282 4.914035 \n",
"10_at 5.070067 2.912126 \n",
"100_at 7.017582 6.905274 \n",
"1000_at 8.754138 6.827789 \n",
"10000_at 4.776181 4.715363 \n",
"10001_at 8.015398 7.107112 \n",
" 5500994157493061613625_A07 5500994157493061613625_A08\n",
"1_at 3.827411 5.147878 \n",
"10_at 3.028838 3.049457 \n",
"100_at 9.751193 7.540148 \n",
"1000_at 3.282731 8.739057 \n",
"10000_at 3.575370 4.213761 \n",
"10001_at 7.659327 6.855786 \n",
" 5500994157493061613625_A09 5500994157493061613625_A10 ⋯\n",
"1_at 3.110751 5.054884 ⋯\n",
"10_at 2.996803 3.487389 ⋯\n",
"100_at 5.773222 3.324055 ⋯\n",
"1000_at 9.572730 3.037323 ⋯\n",
"10000_at 5.838059 2.894429 ⋯\n",
"10001_at 7.808900 7.290094 ⋯\n",
" 5500994175999120813240_H02 5500994175999120813240_H03\n",
"1_at 4.273165 3.442682 \n",
"10_at 3.169651 3.094766 \n",
"100_at 6.993797 8.793967 \n",
"1000_at 3.816762 3.022264 \n",
"10000_at 5.388321 2.827153 \n",
"10001_at 7.876365 8.314665 \n",
" 5500994175999120813240_H04 5500994175999120813240_H05\n",
"1_at 4.923977 2.901377 \n",
"10_at 2.978914 3.312476 \n",
"100_at 11.941098 9.371423 \n",
"1000_at 5.862574 6.649221 \n",
"10000_at 3.599740 5.266808 \n",
"10001_at 8.197616 7.431327 \n",
" 5500994175999120813240_H06 5500994175999120813240_H07\n",
"1_at 4.528475 5.079415 \n",
"10_at 3.271839 3.004895 \n",
"100_at 7.939735 9.046963 \n",
"1000_at 8.565891 6.079522 \n",
"10000_at 3.960827 5.060720 \n",
"10001_at 8.092348 6.973491 \n",
" 5500994175999120813240_H08 5500994175999120813240_H09\n",
"1_at 2.959578 3.094308 \n",
"10_at 3.039933 3.346097 \n",
"100_at 6.055670 7.746151 \n",
"1000_at 4.536474 4.141976 \n",
"10000_at 5.723751 3.494836 \n",
"10001_at 8.852970 8.436557 \n",
" 5500994175999120813240_H10 5500994175999120813240_H11\n",
"1_at 4.045297 5.339831 \n",
"10_at 3.049132 3.238387 \n",
"100_at 6.814890 5.698509 \n",
"1000_at 8.703439 4.722706 \n",
"10000_at 3.297643 5.769323 \n",
"10001_at 7.824003 7.584112 "
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"GDSC_rma_ba <- affy::justRMA(celfile.path=\"arrays/E-MTAB-3610/\",filenames = fnames,sampleNames=snames,\n",
" verbose=FALSE,compress=FALSE,cdfname=customAnno$customCDFname)\n",
"#GDSC_rma_ba\n",
"dim(exprs(GDSC_rma_ba))\n",
"head(exprs(GDSC_rma_ba))"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"'select()' returned 1:1 mapping between keys and columns\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"0 8 NA values in columns PROBEID ENTREZID \n",
"18645 rows remain after removing NA from ENTREZID \n",
"duplicates in column PROBEID 0 \n",
"duplicates in column ENTREZID 0 \n",
"unique genes 18645 \n"
]
},
{
"data": {
"text/html": [
"<ol class=list-inline>\n",
"\t<li>18645</li>\n",
"\t<li>2</li>\n",
"</ol>\n"
],
"text/latex": [
"\\begin{enumerate*}\n",
"\\item 18645\n",
"\\item 2\n",
"\\end{enumerate*}\n"
],
"text/markdown": [
"1. 18645\n",
"2. 2\n",
"\n",
"\n"
],
"text/plain": [
"[1] 18645 2"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"'select()' returned 1:1 mapping between keys and columns\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"0 8 NA values in columns PROBEID SYMBOL \n",
"18645 rows remain after removing NA from SYMBOL \n",
"duplicates in column PROBEID 0 \n",
"duplicates in column SYMBOL 0 \n",
"unique genes 18645 \n"
]
}
],
"source": [
"diagnose_annotation <- function(anno,drop_NA=TRUE){\n",
" \n",
" cat(paste(sum(is.na(anno[,1])),sum(is.na(anno[,2])),\n",
" \"NA values in columns\",colnames(anno)[1],colnames(anno)[2],\"\\n\",sep=\" \"))\n",
" a <- anno[!is.na(anno[,2]),]\n",
" cat(paste(dim(a)[1],\"rows remain after removing NA from \",colnames(anno)[2],\"\\n\",sep=\" \"))\n",
" dups <- unique(a[,1][duplicated(a[,1])])\n",
" cat(paste(\"duplicates in column\",colnames(a)[1], length(dups),\"\\n\",sep=\" \"))\n",
" dup_probes <- unique(a[,2][duplicated(a[,2])])\n",
" cat(paste(\"duplicates in column\",colnames(a)[2], length(dup_probes),\"\\n\",sep=\" \"))\n",
" cat(paste(\"unique genes\",length(unique(a[,2])),\"\\n\",sep=\" \"))\n",
" if (drop_NA){\n",
" # drop unmapped probes with NA gene IDs\n",
" anno <- anno[!is.na(anno[,2]),]\n",
" return(anno)\n",
" }\n",
" else{\n",
" return(anno)\n",
" }\n",
"}\n",
"anno_ENTREZID <- select(get(customAnno$customDBname), keytype=\"PROBEID\", \n",
" columns=c(\"ENTREZID\"), keys=row.names(exprs(GDSC_rma_ba)))\n",
"anno_ENTREZID <- diagnose_annotation(anno_ENTREZID)\n",
"dim(anno_ENTREZID)\n",
"anno_SYMBOL <- select(get(customAnno$customDBname), keytype=\"PROBEID\", \n",
" columns=c(\"SYMBOL\"), keys=row.names(exprs(GDSC_rma_ba)))\n",
"anno_SYMBOL <- diagnose_annotation(anno_SYMBOL)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Annotate probesets with genes and summarize to gene level\n",
"- Use Entrez gene IDs\n",
"- Apply WGCNA::collapseRows(method=\"Average\")\n",
"- write to file"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<ol class=list-inline>\n",
"\t<li>18645</li>\n",
"\t<li>1018</li>\n",
"</ol>\n"
],
"text/latex": [
"\\begin{enumerate*}\n",
"\\item 18645\n",
"\\item 1018\n",
"\\end{enumerate*}\n"
],
"text/markdown": [
"1. 18645\n",
"2. 1018\n",
"\n",
"\n"
],
"text/plain": [
"[1] 18645 1018"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th></th><th scope=col>5500994157493061613625_A01</th><th scope=col>5500994157493061613625_A02</th><th scope=col>5500994157493061613625_A03</th><th scope=col>5500994157493061613625_A04</th><th scope=col>5500994157493061613625_A05</th><th scope=col>5500994157493061613625_A06</th><th scope=col>5500994157493061613625_A07</th><th scope=col>5500994157493061613625_A08</th><th scope=col>5500994157493061613625_A09</th><th scope=col>5500994157493061613625_A10</th><th scope=col>⋯</th><th scope=col>5500994175999120813240_H02</th><th scope=col>5500994175999120813240_H03</th><th scope=col>5500994175999120813240_H04</th><th scope=col>5500994175999120813240_H05</th><th scope=col>5500994175999120813240_H06</th><th scope=col>5500994175999120813240_H07</th><th scope=col>5500994175999120813240_H08</th><th scope=col>5500994175999120813240_H09</th><th scope=col>5500994175999120813240_H10</th><th scope=col>5500994175999120813240_H11</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><th scope=row>A1BG</th><td>6.210671</td><td>5.029226</td><td>5.513632</td><td>4.208249</td><td>3.402282</td><td>4.914035</td><td>3.827411</td><td>5.147878</td><td>3.110751</td><td>5.054884</td><td>⋯ </td><td>4.273165</td><td>3.442682</td><td>4.923977</td><td>2.901377</td><td>4.528475</td><td>5.079415</td><td>2.959578</td><td>3.094308</td><td>4.045297</td><td>5.339831</td></tr>\n",
"\t<tr><th scope=row>A1CF</th><td>2.986196</td><td>2.952698</td><td>2.876904</td><td>3.078416</td><td>2.859689</td><td>3.226181</td><td>3.002562</td><td>2.899220</td><td>2.761808</td><td>2.991242</td><td>⋯ </td><td>2.948285</td><td>3.162107</td><td>2.989301</td><td>3.122200</td><td>2.981742</td><td>2.912033</td><td>2.950125</td><td>2.788239</td><td>2.874734</td><td>2.930411</td></tr>\n",
"\t<tr><th scope=row>A2M</th><td>3.138822</td><td>3.339745</td><td>3.288143</td><td>3.035124</td><td>3.266711</td><td>6.878105</td><td>3.306808</td><td>3.376042</td><td>3.326467</td><td>3.532250</td><td>⋯ </td><td>3.898669</td><td>3.478617</td><td>3.251410</td><td>6.346759</td><td>3.532383</td><td>3.161646</td><td>3.203922</td><td>3.483303</td><td>5.147751</td><td>8.860099</td></tr>\n",
"\t<tr><th scope=row>A2ML1</th><td>2.659014</td><td>2.740146</td><td>3.941870</td><td>2.782538</td><td>2.716182</td><td>2.912234</td><td>2.791071</td><td>2.829216</td><td>2.736346</td><td>2.977346</td><td>⋯ </td><td>2.904620</td><td>2.795384</td><td>2.714010</td><td>2.835382</td><td>2.763315</td><td>2.752095</td><td>2.911493</td><td>2.920386</td><td>2.794910</td><td>2.991144</td></tr>\n",
"\t<tr><th scope=row>A3GALT2</th><td>2.765093</td><td>2.871171</td><td>3.009816</td><td>2.634662</td><td>2.697715</td><td>2.593990</td><td>2.929163</td><td>2.744387</td><td>2.998624</td><td>3.043765</td><td>⋯ </td><td>2.964269</td><td>3.067023</td><td>2.768809</td><td>2.607127</td><td>2.778964</td><td>2.850118</td><td>2.703913</td><td>2.663925</td><td>2.763491</td><td>2.604637</td></tr>\n",
"\t<tr><th scope=row>A4GALT</th><td>3.342432</td><td>3.138229</td><td>3.513538</td><td>3.166587</td><td>3.240146</td><td>3.246475</td><td>3.801788</td><td>3.377124</td><td>3.288002</td><td>3.361292</td><td>⋯ </td><td>3.384112</td><td>3.070601</td><td>2.986975</td><td>3.334498</td><td>3.398661</td><td>3.195717</td><td>3.277447</td><td>4.407162</td><td>3.008970</td><td>3.053538</td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|llllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllll}\n",
" & 5500994157493061613625\\_A01 & 5500994157493061613625\\_A02 & 5500994157493061613625\\_A03 & 5500994157493061613625\\_A04 & 5500994157493061613625\\_A05 & 5500994157493061613625\\_A06 & 5500994157493061613625\\_A07 & 5500994157493061613625\\_A08 & 5500994157493061613625\\_A09 & 5500994157493061613625\\_A10 & ⋯ & 5500994175999120813240\\_H02 & 5500994175999120813240\\_H03 & 5500994175999120813240\\_H04 & 5500994175999120813240\\_H05 & 5500994175999120813240\\_H06 & 5500994175999120813240\\_H07 & 5500994175999120813240\\_H08 & 5500994175999120813240\\_H09 & 5500994175999120813240\\_H10 & 5500994175999120813240\\_H11\\\\\n",
"\\hline\n",
"\tA1BG & 6.210671 & 5.029226 & 5.513632 & 4.208249 & 3.402282 & 4.914035 & 3.827411 & 5.147878 & 3.110751 & 5.054884 & ⋯ & 4.273165 & 3.442682 & 4.923977 & 2.901377 & 4.528475 & 5.079415 & 2.959578 & 3.094308 & 4.045297 & 5.339831\\\\\n",
"\tA1CF & 2.986196 & 2.952698 & 2.876904 & 3.078416 & 2.859689 & 3.226181 & 3.002562 & 2.899220 & 2.761808 & 2.991242 & ⋯ & 2.948285 & 3.162107 & 2.989301 & 3.122200 & 2.981742 & 2.912033 & 2.950125 & 2.788239 & 2.874734 & 2.930411\\\\\n",
"\tA2M & 3.138822 & 3.339745 & 3.288143 & 3.035124 & 3.266711 & 6.878105 & 3.306808 & 3.376042 & 3.326467 & 3.532250 & ⋯ & 3.898669 & 3.478617 & 3.251410 & 6.346759 & 3.532383 & 3.161646 & 3.203922 & 3.483303 & 5.147751 & 8.860099\\\\\n",
"\tA2ML1 & 2.659014 & 2.740146 & 3.941870 & 2.782538 & 2.716182 & 2.912234 & 2.791071 & 2.829216 & 2.736346 & 2.977346 & ⋯ & 2.904620 & 2.795384 & 2.714010 & 2.835382 & 2.763315 & 2.752095 & 2.911493 & 2.920386 & 2.794910 & 2.991144\\\\\n",
"\tA3GALT2 & 2.765093 & 2.871171 & 3.009816 & 2.634662 & 2.697715 & 2.593990 & 2.929163 & 2.744387 & 2.998624 & 3.043765 & ⋯ & 2.964269 & 3.067023 & 2.768809 & 2.607127 & 2.778964 & 2.850118 & 2.703913 & 2.663925 & 2.763491 & 2.604637\\\\\n",
"\tA4GALT & 3.342432 & 3.138229 & 3.513538 & 3.166587 & 3.240146 & 3.246475 & 3.801788 & 3.377124 & 3.288002 & 3.361292 & ⋯ & 3.384112 & 3.070601 & 2.986975 & 3.334498 & 3.398661 & 3.195717 & 3.277447 & 4.407162 & 3.008970 & 3.053538\\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"| <!--/--> | 5500994157493061613625_A01 | 5500994157493061613625_A02 | 5500994157493061613625_A03 | 5500994157493061613625_A04 | 5500994157493061613625_A05 | 5500994157493061613625_A06 | 5500994157493061613625_A07 | 5500994157493061613625_A08 | 5500994157493061613625_A09 | 5500994157493061613625_A10 | ⋯ | 5500994175999120813240_H02 | 5500994175999120813240_H03 | 5500994175999120813240_H04 | 5500994175999120813240_H05 | 5500994175999120813240_H06 | 5500994175999120813240_H07 | 5500994175999120813240_H08 | 5500994175999120813240_H09 | 5500994175999120813240_H10 | 5500994175999120813240_H11 | \n",
"|---|---|---|---|---|---|\n",
"| A1BG | 6.210671 | 5.029226 | 5.513632 | 4.208249 | 3.402282 | 4.914035 | 3.827411 | 5.147878 | 3.110751 | 5.054884 | ⋯ | 4.273165 | 3.442682 | 4.923977 | 2.901377 | 4.528475 | 5.079415 | 2.959578 | 3.094308 | 4.045297 | 5.339831 | \n",
"| A1CF | 2.986196 | 2.952698 | 2.876904 | 3.078416 | 2.859689 | 3.226181 | 3.002562 | 2.899220 | 2.761808 | 2.991242 | ⋯ | 2.948285 | 3.162107 | 2.989301 | 3.122200 | 2.981742 | 2.912033 | 2.950125 | 2.788239 | 2.874734 | 2.930411 | \n",
"| A2M | 3.138822 | 3.339745 | 3.288143 | 3.035124 | 3.266711 | 6.878105 | 3.306808 | 3.376042 | 3.326467 | 3.532250 | ⋯ | 3.898669 | 3.478617 | 3.251410 | 6.346759 | 3.532383 | 3.161646 | 3.203922 | 3.483303 | 5.147751 | 8.860099 | \n",
"| A2ML1 | 2.659014 | 2.740146 | 3.941870 | 2.782538 | 2.716182 | 2.912234 | 2.791071 | 2.829216 | 2.736346 | 2.977346 | ⋯ | 2.904620 | 2.795384 | 2.714010 | 2.835382 | 2.763315 | 2.752095 | 2.911493 | 2.920386 | 2.794910 | 2.991144 | \n",
"| A3GALT2 | 2.765093 | 2.871171 | 3.009816 | 2.634662 | 2.697715 | 2.593990 | 2.929163 | 2.744387 | 2.998624 | 3.043765 | ⋯ | 2.964269 | 3.067023 | 2.768809 | 2.607127 | 2.778964 | 2.850118 | 2.703913 | 2.663925 | 2.763491 | 2.604637 | \n",
"| A4GALT | 3.342432 | 3.138229 | 3.513538 | 3.166587 | 3.240146 | 3.246475 | 3.801788 | 3.377124 | 3.288002 | 3.361292 | ⋯ | 3.384112 | 3.070601 | 2.986975 | 3.334498 | 3.398661 | 3.195717 | 3.277447 | 4.407162 | 3.008970 | 3.053538 | \n",
"\n",
"\n"
],
"text/plain": [
" 5500994157493061613625_A01 5500994157493061613625_A02\n",
"A1BG 6.210671 5.029226 \n",
"A1CF 2.986196 2.952698 \n",
"A2M 3.138822 3.339745 \n",
"A2ML1 2.659014 2.740146 \n",
"A3GALT2 2.765093 2.871171 \n",
"A4GALT 3.342432 3.138229 \n",
" 5500994157493061613625_A03 5500994157493061613625_A04\n",
"A1BG 5.513632 4.208249 \n",
"A1CF 2.876904 3.078416 \n",
"A2M 3.288143 3.035124 \n",
"A2ML1 3.941870 2.782538 \n",
"A3GALT2 3.009816 2.634662 \n",
"A4GALT 3.513538 3.166587 \n",
" 5500994157493061613625_A05 5500994157493061613625_A06\n",
"A1BG 3.402282 4.914035 \n",
"A1CF 2.859689 3.226181 \n",
"A2M 3.266711 6.878105 \n",
"A2ML1 2.716182 2.912234 \n",
"A3GALT2 2.697715 2.593990 \n",
"A4GALT 3.240146 3.246475 \n",
" 5500994157493061613625_A07 5500994157493061613625_A08\n",
"A1BG 3.827411 5.147878 \n",
"A1CF 3.002562 2.899220 \n",
"A2M 3.306808 3.376042 \n",
"A2ML1 2.791071 2.829216 \n",
"A3GALT2 2.929163 2.744387 \n",
"A4GALT 3.801788 3.377124 \n",
" 5500994157493061613625_A09 5500994157493061613625_A10 ⋯\n",
"A1BG 3.110751 5.054884 ⋯\n",
"A1CF 2.761808 2.991242 ⋯\n",
"A2M 3.326467 3.532250 ⋯\n",
"A2ML1 2.736346 2.977346 ⋯\n",
"A3GALT2 2.998624 3.043765 ⋯\n",
"A4GALT 3.288002 3.361292 ⋯\n",
" 5500994175999120813240_H02 5500994175999120813240_H03\n",
"A1BG 4.273165 3.442682 \n",
"A1CF 2.948285 3.162107 \n",
"A2M 3.898669 3.478617 \n",
"A2ML1 2.904620 2.795384 \n",
"A3GALT2 2.964269 3.067023 \n",
"A4GALT 3.384112 3.070601 \n",
" 5500994175999120813240_H04 5500994175999120813240_H05\n",
"A1BG 4.923977 2.901377 \n",
"A1CF 2.989301 3.122200 \n",
"A2M 3.251410 6.346759 \n",
"A2ML1 2.714010 2.835382 \n",
"A3GALT2 2.768809 2.607127 \n",
"A4GALT 2.986975 3.334498 \n",
" 5500994175999120813240_H06 5500994175999120813240_H07\n",
"A1BG 4.528475 5.079415 \n",
"A1CF 2.981742 2.912033 \n",
"A2M 3.532383 3.161646 \n",
"A2ML1 2.763315 2.752095 \n",
"A3GALT2 2.778964 2.850118 \n",
"A4GALT 3.398661 3.195717 \n",
" 5500994175999120813240_H08 5500994175999120813240_H09\n",
"A1BG 2.959578 3.094308 \n",
"A1CF 2.950125 2.788239 \n",
"A2M 3.203922 3.483303 \n",
"A2ML1 2.911493 2.920386 \n",
"A3GALT2 2.703913 2.663925 \n",
"A4GALT 3.277447 4.407162 \n",
" 5500994175999120813240_H10 5500994175999120813240_H11\n",
"A1BG 4.045297 5.339831 \n",
"A1CF 2.874734 2.930411 \n",
"A2M 5.147751 8.860099 \n",
"A2ML1 2.794910 2.991144 \n",
"A3GALT2 2.763491 2.604637 \n",
"A4GALT 3.008970 3.053538 "
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"# actually, no CollapseRows() needed here, because these mappings are one-to-one\n",
"CR <- WGCNA::collapseRows(exprs(GDSC_RMA_BrainArray), rowGroup = anno_ENTREZID$ENTREZID,\n",
" rowID = anno_ENTREZID$PROBEID,method=\"Average\")\n",
"exprs_GDSC_RMA_BrainArray_ENTREZ <- CR$datETcollapsed\n",
"\n",
"# the same for SYMBOL\n",
"CR <- WGCNA::collapseRows(exprs(GDSC_RMA_BrainArray), rowGroup = anno_SYMBOL$SYMBOL,\n",
" rowID = anno_SYMBOL$PROBEID,method=\"Average\")\n",
"exprs_GDSC_RMA_BrainArray_SYMBOL <- CR$datETcollapsed\n",
"\n",
"dim(exprs_GDSC_RMA_BrainArray_SYMBOL)\n",
"head(exprs_GDSC_RMA_BrainArray_SYMBOL)\n",
"write.table(exprs_GDSC_RMA_BrainArray_SYMBOL, file =\"Geeleher_with_GDSCr6/data/GDSC_micro.BrainArray.RMAlog2Average.Symbol.Expr.tsv\"\n",
" ,na=\"\",quote = FALSE,sep=\"\\t\")\n",
"write.table(exprs_GDSC_RMA_BrainArray_ENTREZ, file =\"Geeleher_with_GDSCr6/data/GDSC_micro.BrainArray.RMAlog2Average.Entrez.Expr.tsv\"\n",
" ,na=\"\",quote = FALSE,sep=\"\\t\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Compare with Lukas's data "
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<ol class=list-inline>\n",
"\t<li>17419</li>\n",
"\t<li>962</li>\n",
"</ol>\n"
],
"text/latex": [
"\\begin{enumerate*}\n",
"\\item 17419\n",
"\\item 962\n",
"\\end{enumerate*}\n"
],
"text/markdown": [
"1. 17419\n",
"2. 962\n",
"\n",
"\n"
],
"text/plain": [
"[1] 17419 962"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th></th><th scope=col>CAL.120</th><th scope=col>DMS.114</th><th scope=col>CAL.51</th><th scope=col>H2869</th><th scope=col>H290</th><th scope=col>A2058</th><th scope=col>CESS</th><th scope=col>H2803</th><th scope=col>H2722</th><th scope=col>HCC1419</th><th scope=col>⋯</th><th scope=col>SW1271</th><th scope=col>NCI.H716</th><th scope=col>LB831.BLC</th><th scope=col>HC.1</th><th scope=col>Jurkat</th><th scope=col>MOG.G.UVW</th><th scope=col>JIMT.1</th><th scope=col>PEO1</th><th scope=col>PL4</th><th scope=col>TT</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><th scope=row>TSPAN6</th><td> 7.632023</td><td> 7.548671</td><td>8.712338 </td><td>7.797142 </td><td> 7.729268</td><td>7.074533 </td><td> 3.285198</td><td> 6.961606</td><td> 5.943046</td><td> 3.455951</td><td>⋯ </td><td> 6.287819</td><td> 3.607123</td><td> 7.105637</td><td> 3.236503</td><td> 3.038892</td><td> 8.373223</td><td> 8.441628</td><td> 8.422922</td><td> 8.089255</td><td>3.112333 </td></tr>\n",
"\t<tr><th scope=row>TNMD</th><td> 2.964585</td><td> 2.777716</td><td>2.643508 </td><td>2.817923 </td><td> 2.957739</td><td>2.889677 </td><td> 2.828203</td><td> 2.874751</td><td> 2.686874</td><td> 3.290184</td><td>⋯ </td><td> 2.842090</td><td> 2.866483</td><td> 2.798847</td><td> 2.745137</td><td> 2.976406</td><td> 2.852552</td><td> 2.639276</td><td> 2.879890</td><td> 2.521169</td><td>2.870468 </td></tr>\n",
"\t<tr><th scope=row>DPM1</th><td>10.379553</td><td>11.807341</td><td>9.880733 </td><td>9.883471 </td><td>10.418840</td><td>9.773987 </td><td>10.264385</td><td>10.205931</td><td>10.299757</td><td>11.570155</td><td>⋯ </td><td>10.370130</td><td>10.246750</td><td>10.486486</td><td>10.442951</td><td>10.311962</td><td>10.454830</td><td>11.463742</td><td>10.557777</td><td>10.792750</td><td>9.873902 </td></tr>\n",
"\t<tr><th scope=row>SCYL3</th><td> 3.614794</td><td> 4.066887</td><td>3.956230 </td><td>4.063701 </td><td> 4.341500</td><td>4.270903 </td><td> 5.968168</td><td> 3.715033</td><td> 3.848112</td><td> 5.560883</td><td>⋯ </td><td> 3.789814</td><td> 3.780485</td><td> 3.696835</td><td> 4.624013</td><td> 4.348524</td><td> 3.858121</td><td> 4.425849</td><td> 3.550390</td><td> 4.443337</td><td>4.266828 </td></tr>\n",
"\t<tr><th scope=row>C1orf112</th><td> 3.380681</td><td> 3.732485</td><td>3.236620 </td><td>3.558414 </td><td> 3.840373</td><td>3.815055 </td><td> 3.011867</td><td> 3.268449</td><td> 3.352835</td><td> 3.571228</td><td>⋯ </td><td> 3.318119</td><td> 3.499160</td><td> 3.726833</td><td> 3.947744</td><td> 3.806584</td><td> 3.196988</td><td> 4.384732</td><td> 4.247189</td><td> 3.071359</td><td>3.230197 </td></tr>\n",
"\t<tr><th scope=row>FGR</th><td> 3.324692</td><td> 3.152404</td><td>3.241246 </td><td>3.101247 </td><td> 3.001802</td><td>3.298915 </td><td> 9.565308</td><td> 3.036333</td><td> 3.278688</td><td> 3.370885</td><td>⋯ </td><td> 3.154849</td><td> 3.056503</td><td> 3.245301</td><td> 8.969347</td><td> 3.562548</td><td> 3.098083</td><td> 3.229511</td><td> 3.176336</td><td> 3.238305</td><td>3.027742 </td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|llllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllll}\n",
" & CAL.120 & DMS.114 & CAL.51 & H2869 & H290 & A2058 & CESS & H2803 & H2722 & HCC1419 & ⋯ & SW1271 & NCI.H716 & LB831.BLC & HC.1 & Jurkat & MOG.G.UVW & JIMT.1 & PEO1 & PL4 & TT\\\\\n",
"\\hline\n",
"\tTSPAN6 & 7.632023 & 7.548671 & 8.712338 & 7.797142 & 7.729268 & 7.074533 & 3.285198 & 6.961606 & 5.943046 & 3.455951 & ⋯ & 6.287819 & 3.607123 & 7.105637 & 3.236503 & 3.038892 & 8.373223 & 8.441628 & 8.422922 & 8.089255 & 3.112333 \\\\\n",
"\tTNMD & 2.964585 & 2.777716 & 2.643508 & 2.817923 & 2.957739 & 2.889677 & 2.828203 & 2.874751 & 2.686874 & 3.290184 & ⋯ & 2.842090 & 2.866483 & 2.798847 & 2.745137 & 2.976406 & 2.852552 & 2.639276 & 2.879890 & 2.521169 & 2.870468 \\\\\n",
"\tDPM1 & 10.379553 & 11.807341 & 9.880733 & 9.883471 & 10.418840 & 9.773987 & 10.264385 & 10.205931 & 10.299757 & 11.570155 & ⋯ & 10.370130 & 10.246750 & 10.486486 & 10.442951 & 10.311962 & 10.454830 & 11.463742 & 10.557777 & 10.792750 & 9.873902 \\\\\n",
"\tSCYL3 & 3.614794 & 4.066887 & 3.956230 & 4.063701 & 4.341500 & 4.270903 & 5.968168 & 3.715033 & 3.848112 & 5.560883 & ⋯ & 3.789814 & 3.780485 & 3.696835 & 4.624013 & 4.348524 & 3.858121 & 4.425849 & 3.550390 & 4.443337 & 4.266828 \\\\\n",
"\tC1orf112 & 3.380681 & 3.732485 & 3.236620 & 3.558414 & 3.840373 & 3.815055 & 3.011867 & 3.268449 & 3.352835 & 3.571228 & ⋯ & 3.318119 & 3.499160 & 3.726833 & 3.947744 & 3.806584 & 3.196988 & 4.384732 & 4.247189 & 3.071359 & 3.230197 \\\\\n",
"\tFGR & 3.324692 & 3.152404 & 3.241246 & 3.101247 & 3.001802 & 3.298915 & 9.565308 & 3.036333 & 3.278688 & 3.370885 & ⋯ & 3.154849 & 3.056503 & 3.245301 & 8.969347 & 3.562548 & 3.098083 & 3.229511 & 3.176336 & 3.238305 & 3.027742 \\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"| <!--/--> | CAL.120 | DMS.114 | CAL.51 | H2869 | H290 | A2058 | CESS | H2803 | H2722 | HCC1419 | ⋯ | SW1271 | NCI.H716 | LB831.BLC | HC.1 | Jurkat | MOG.G.UVW | JIMT.1 | PEO1 | PL4 | TT | \n",
"|---|---|---|---|---|---|\n",
"| TSPAN6 | 7.632023 | 7.548671 | 8.712338 | 7.797142 | 7.729268 | 7.074533 | 3.285198 | 6.961606 | 5.943046 | 3.455951 | ⋯ | 6.287819 | 3.607123 | 7.105637 | 3.236503 | 3.038892 | 8.373223 | 8.441628 | 8.422922 | 8.089255 | 3.112333 | \n",
"| TNMD | 2.964585 | 2.777716 | 2.643508 | 2.817923 | 2.957739 | 2.889677 | 2.828203 | 2.874751 | 2.686874 | 3.290184 | ⋯ | 2.842090 | 2.866483 | 2.798847 | 2.745137 | 2.976406 | 2.852552 | 2.639276 | 2.879890 | 2.521169 | 2.870468 | \n",
"| DPM1 | 10.379553 | 11.807341 | 9.880733 | 9.883471 | 10.418840 | 9.773987 | 10.264385 | 10.205931 | 10.299757 | 11.570155 | ⋯ | 10.370130 | 10.246750 | 10.486486 | 10.442951 | 10.311962 | 10.454830 | 11.463742 | 10.557777 | 10.792750 | 9.873902 | \n",
"| SCYL3 | 3.614794 | 4.066887 | 3.956230 | 4.063701 | 4.341500 | 4.270903 | 5.968168 | 3.715033 | 3.848112 | 5.560883 | ⋯ | 3.789814 | 3.780485 | 3.696835 | 4.624013 | 4.348524 | 3.858121 | 4.425849 | 3.550390 | 4.443337 | 4.266828 | \n",
"| C1orf112 | 3.380681 | 3.732485 | 3.236620 | 3.558414 | 3.840373 | 3.815055 | 3.011867 | 3.268449 | 3.352835 | 3.571228 | ⋯ | 3.318119 | 3.499160 | 3.726833 | 3.947744 | 3.806584 | 3.196988 | 4.384732 | 4.247189 | 3.071359 | 3.230197 | \n",
"| FGR | 3.324692 | 3.152404 | 3.241246 | 3.101247 | 3.001802 | 3.298915 | 9.565308 | 3.036333 | 3.278688 | 3.370885 | ⋯ | 3.154849 | 3.056503 | 3.245301 | 8.969347 | 3.562548 | 3.098083 | 3.229511 | 3.176336 | 3.238305 | 3.027742 | \n",
"\n",
"\n"
],
"text/plain": [
" CAL.120 DMS.114 CAL.51 H2869 H290 A2058 CESS \n",
"TSPAN6 7.632023 7.548671 8.712338 7.797142 7.729268 7.074533 3.285198\n",
"TNMD 2.964585 2.777716 2.643508 2.817923 2.957739 2.889677 2.828203\n",
"DPM1 10.379553 11.807341 9.880733 9.883471 10.418840 9.773987 10.264385\n",
"SCYL3 3.614794 4.066887 3.956230 4.063701 4.341500 4.270903 5.968168\n",
"C1orf112 3.380681 3.732485 3.236620 3.558414 3.840373 3.815055 3.011867\n",
"FGR 3.324692 3.152404 3.241246 3.101247 3.001802 3.298915 9.565308\n",
" H2803 H2722 HCC1419 ⋯ SW1271 NCI.H716 LB831.BLC\n",
"TSPAN6 6.961606 5.943046 3.455951 ⋯ 6.287819 3.607123 7.105637\n",
"TNMD 2.874751 2.686874 3.290184 ⋯ 2.842090 2.866483 2.798847\n",
"DPM1 10.205931 10.299757 11.570155 ⋯ 10.370130 10.246750 10.486486\n",
"SCYL3 3.715033 3.848112 5.560883 ⋯ 3.789814 3.780485 3.696835\n",
"C1orf112 3.268449 3.352835 3.571228 ⋯ 3.318119 3.499160 3.726833\n",
"FGR 3.036333 3.278688 3.370885 ⋯ 3.154849 3.056503 3.245301\n",
" HC.1 Jurkat MOG.G.UVW JIMT.1 PEO1 PL4 TT \n",
"TSPAN6 3.236503 3.038892 8.373223 8.441628 8.422922 8.089255 3.112333\n",
"TNMD 2.745137 2.976406 2.852552 2.639276 2.879890 2.521169 2.870468\n",
"DPM1 10.442951 10.311962 10.454830 11.463742 10.557777 10.792750 9.873902\n",
"SCYL3 4.624013 4.348524 3.858121 4.425849 3.550390 4.443337 4.266828\n",
"C1orf112 3.947744 3.806584 3.196988 4.384732 4.247189 3.071359 3.230197\n",
"FGR 8.969347 3.562548 3.098083 3.229511 3.176336 3.238305 3.027742"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"GEX <- read.csv(\"Geeleher_with_GDSCr6/data/GEX.csv\",row.names=1,header = T)\n",
"dim(GEX)\n",
"head(GEX)"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [
{
"data": {
"image/png": 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1BiOb4gWjBM+svty3UiN2sQlljEtW2UEjnV9BBhfbBeqD/K9qXqs4EocBqWfrra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\nAABJRU5ErkJggg==",
"text/plain": [
"Plot with title “our results”"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"myhist <- function(expr,title = \"Histogram\", xlabel = \"RMAlog2\"){\n",
" i=1 \n",
" plot( density(expr[,i]),main = title, xlab=xlabel)\n",
" for(i in 2:dim(expr)[2]){\n",
" lines(density((expr[,i])))\n",
" }\n",
"}\n",
"options(repr.plot.width=10, repr.plot.height=3)\n",
"par(mfrow = c(1,2))\n",
"myhist(GEX, title = \"GEX\")\n",
"myhist(exprs_GDSC_RMA_BrainArray_SYMBOL, title = \"our results\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Compare two expression marices after annotatation\n",
"(now they have mostly the same row.names)\n",
" - find the number of rows in each and the number of shared row names \n",
" - correlation of gene profiles\n",
" - correlation of sample profiles"
]
},
{
"cell_type": "code",
"execution_count": 67,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th></th><th scope=col>5500994157493061613625_A01</th><th scope=col>5500994157493061613625_A02</th><th scope=col>5500994157493061613625_A03</th><th scope=col>5500994157493061613625_A04</th><th scope=col>5500994157493061613625_A05</th><th scope=col>5500994157493061613625_A06</th><th scope=col>5500994157493061613625_A07</th><th scope=col>5500994157493061613625_A08</th><th scope=col>5500994157493061613625_A09</th><th scope=col>5500994157493061613625_A10</th><th scope=col>⋯</th><th scope=col>5500994175999120813240_H02</th><th scope=col>5500994175999120813240_H03</th><th scope=col>5500994175999120813240_H04</th><th scope=col>5500994175999120813240_H05</th><th scope=col>5500994175999120813240_H06</th><th scope=col>5500994175999120813240_H07</th><th scope=col>5500994175999120813240_H08</th><th scope=col>5500994175999120813240_H09</th><th scope=col>5500994175999120813240_H10</th><th scope=col>5500994175999120813240_H11</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><th scope=row>A1BG</th><td>6,210671</td><td>5,029226</td><td>5,513632</td><td>4,208249</td><td>3,402282</td><td>4,914035</td><td>3,827411</td><td>5,147878</td><td>3,110751</td><td>5,054884</td><td>⋯ </td><td>4,273165</td><td>3,442682</td><td>4,923977</td><td>2,901377</td><td>4,528475</td><td>5,079415</td><td>2,959578</td><td>3,094308</td><td>4,045297</td><td>5,339831</td></tr>\n",
"\t<tr><th scope=row>A1CF</th><td>2,986196</td><td>2,952698</td><td>2,876904</td><td>3,078416</td><td>2,859689</td><td>3,226181</td><td>3,002562</td><td>2,899220</td><td>2,761808</td><td>2,991242</td><td>⋯ </td><td>2,948285</td><td>3,162107</td><td>2,989301</td><td>3,122200</td><td>2,981742</td><td>2,912033</td><td>2,950125</td><td>2,788239</td><td>2,874734</td><td>2,930411</td></tr>\n",
"\t<tr><th scope=row>A2M</th><td>3,138822</td><td>3,339745</td><td>3,288143</td><td>3,035124</td><td>3,266711</td><td>6,878105</td><td>3,306808</td><td>3,376042</td><td>3,326467</td><td>3,532250</td><td>⋯ </td><td>3,898669</td><td>3,478617</td><td>3,251410</td><td>6,346759</td><td>3,532383</td><td>3,161646</td><td>3,203922</td><td>3,483303</td><td>5,147751</td><td>8,860099</td></tr>\n",
"\t<tr><th scope=row>A2ML1</th><td>2,659014</td><td>2,740146</td><td>3,941870</td><td>2,782538</td><td>2,716182</td><td>2,912234</td><td>2,791071</td><td>2,829216</td><td>2,736346</td><td>2,977346</td><td>⋯ </td><td>2,904620</td><td>2,795384</td><td>2,714010</td><td>2,835382</td><td>2,763315</td><td>2,752095</td><td>2,911493</td><td>2,920386</td><td>2,794910</td><td>2,991144</td></tr>\n",
"\t<tr><th scope=row>A3GALT2</th><td>2,765093</td><td>2,871171</td><td>3,009816</td><td>2,634662</td><td>2,697715</td><td>2,593990</td><td>2,929163</td><td>2,744387</td><td>2,998624</td><td>3,043765</td><td>⋯ </td><td>2,964269</td><td>3,067023</td><td>2,768809</td><td>2,607127</td><td>2,778964</td><td>2,850118</td><td>2,703913</td><td>2,663925</td><td>2,763491</td><td>2,604637</td></tr>\n",
"\t<tr><th scope=row>A4GALT</th><td>3,342432</td><td>3,138229</td><td>3,513538</td><td>3,166587</td><td>3,240146</td><td>3,246475</td><td>3,801788</td><td>3,377124</td><td>3,288002</td><td>3,361292</td><td>⋯ </td><td>3,384112</td><td>3,070601</td><td>2,986975</td><td>3,334498</td><td>3,398661</td><td>3,195717</td><td>3,277447</td><td>4,407162</td><td>3,008970</td><td>3,053538</td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|llllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllll}\n",
" & 5500994157493061613625\\_A01 & 5500994157493061613625\\_A02 & 5500994157493061613625\\_A03 & 5500994157493061613625\\_A04 & 5500994157493061613625\\_A05 & 5500994157493061613625\\_A06 & 5500994157493061613625\\_A07 & 5500994157493061613625\\_A08 & 5500994157493061613625\\_A09 & 5500994157493061613625\\_A10 & ⋯ & 5500994175999120813240\\_H02 & 5500994175999120813240\\_H03 & 5500994175999120813240\\_H04 & 5500994175999120813240\\_H05 & 5500994175999120813240\\_H06 & 5500994175999120813240\\_H07 & 5500994175999120813240\\_H08 & 5500994175999120813240\\_H09 & 5500994175999120813240\\_H10 & 5500994175999120813240\\_H11\\\\\n",
"\\hline\n",
"\tA1BG & 6,210671 & 5,029226 & 5,513632 & 4,208249 & 3,402282 & 4,914035 & 3,827411 & 5,147878 & 3,110751 & 5,054884 & ⋯ & 4,273165 & 3,442682 & 4,923977 & 2,901377 & 4,528475 & 5,079415 & 2,959578 & 3,094308 & 4,045297 & 5,339831\\\\\n",
"\tA1CF & 2,986196 & 2,952698 & 2,876904 & 3,078416 & 2,859689 & 3,226181 & 3,002562 & 2,899220 & 2,761808 & 2,991242 & ⋯ & 2,948285 & 3,162107 & 2,989301 & 3,122200 & 2,981742 & 2,912033 & 2,950125 & 2,788239 & 2,874734 & 2,930411\\\\\n",
"\tA2M & 3,138822 & 3,339745 & 3,288143 & 3,035124 & 3,266711 & 6,878105 & 3,306808 & 3,376042 & 3,326467 & 3,532250 & ⋯ & 3,898669 & 3,478617 & 3,251410 & 6,346759 & 3,532383 & 3,161646 & 3,203922 & 3,483303 & 5,147751 & 8,860099\\\\\n",
"\tA2ML1 & 2,659014 & 2,740146 & 3,941870 & 2,782538 & 2,716182 & 2,912234 & 2,791071 & 2,829216 & 2,736346 & 2,977346 & ⋯ & 2,904620 & 2,795384 & 2,714010 & 2,835382 & 2,763315 & 2,752095 & 2,911493 & 2,920386 & 2,794910 & 2,991144\\\\\n",
"\tA3GALT2 & 2,765093 & 2,871171 & 3,009816 & 2,634662 & 2,697715 & 2,593990 & 2,929163 & 2,744387 & 2,998624 & 3,043765 & ⋯ & 2,964269 & 3,067023 & 2,768809 & 2,607127 & 2,778964 & 2,850118 & 2,703913 & 2,663925 & 2,763491 & 2,604637\\\\\n",
"\tA4GALT & 3,342432 & 3,138229 & 3,513538 & 3,166587 & 3,240146 & 3,246475 & 3,801788 & 3,377124 & 3,288002 & 3,361292 & ⋯ & 3,384112 & 3,070601 & 2,986975 & 3,334498 & 3,398661 & 3,195717 & 3,277447 & 4,407162 & 3,008970 & 3,053538\\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"| <!--/--> | 5500994157493061613625_A01 | 5500994157493061613625_A02 | 5500994157493061613625_A03 | 5500994157493061613625_A04 | 5500994157493061613625_A05 | 5500994157493061613625_A06 | 5500994157493061613625_A07 | 5500994157493061613625_A08 | 5500994157493061613625_A09 | 5500994157493061613625_A10 | ⋯ | 5500994175999120813240_H02 | 5500994175999120813240_H03 | 5500994175999120813240_H04 | 5500994175999120813240_H05 | 5500994175999120813240_H06 | 5500994175999120813240_H07 | 5500994175999120813240_H08 | 5500994175999120813240_H09 | 5500994175999120813240_H10 | 5500994175999120813240_H11 | \n",
"|---|---|---|---|---|---|\n",
"| A1BG | 6,210671 | 5,029226 | 5,513632 | 4,208249 | 3,402282 | 4,914035 | 3,827411 | 5,147878 | 3,110751 | 5,054884 | ⋯ | 4,273165 | 3,442682 | 4,923977 | 2,901377 | 4,528475 | 5,079415 | 2,959578 | 3,094308 | 4,045297 | 5,339831 | \n",
"| A1CF | 2,986196 | 2,952698 | 2,876904 | 3,078416 | 2,859689 | 3,226181 | 3,002562 | 2,899220 | 2,761808 | 2,991242 | ⋯ | 2,948285 | 3,162107 | 2,989301 | 3,122200 | 2,981742 | 2,912033 | 2,950125 | 2,788239 | 2,874734 | 2,930411 | \n",
"| A2M | 3,138822 | 3,339745 | 3,288143 | 3,035124 | 3,266711 | 6,878105 | 3,306808 | 3,376042 | 3,326467 | 3,532250 | ⋯ | 3,898669 | 3,478617 | 3,251410 | 6,346759 | 3,532383 | 3,161646 | 3,203922 | 3,483303 | 5,147751 | 8,860099 | \n",
"| A2ML1 | 2,659014 | 2,740146 | 3,941870 | 2,782538 | 2,716182 | 2,912234 | 2,791071 | 2,829216 | 2,736346 | 2,977346 | ⋯ | 2,904620 | 2,795384 | 2,714010 | 2,835382 | 2,763315 | 2,752095 | 2,911493 | 2,920386 | 2,794910 | 2,991144 | \n",
"| A3GALT2 | 2,765093 | 2,871171 | 3,009816 | 2,634662 | 2,697715 | 2,593990 | 2,929163 | 2,744387 | 2,998624 | 3,043765 | ⋯ | 2,964269 | 3,067023 | 2,768809 | 2,607127 | 2,778964 | 2,850118 | 2,703913 | 2,663925 | 2,763491 | 2,604637 | \n",
"| A4GALT | 3,342432 | 3,138229 | 3,513538 | 3,166587 | 3,240146 | 3,246475 | 3,801788 | 3,377124 | 3,288002 | 3,361292 | ⋯ | 3,384112 | 3,070601 | 2,986975 | 3,334498 | 3,398661 | 3,195717 | 3,277447 | 4,407162 | 3,008970 | 3,053538 | \n",
"\n",
"\n"
],
"text/plain": [
" 5500994157493061613625_A01 5500994157493061613625_A02\n",
"A1BG 6,210671 5,029226 \n",
"A1CF 2,986196 2,952698 \n",
"A2M 3,138822 3,339745 \n",
"A2ML1 2,659014 2,740146 \n",
"A3GALT2 2,765093 2,871171 \n",
"A4GALT 3,342432 3,138229 \n",
" 5500994157493061613625_A03 5500994157493061613625_A04\n",
"A1BG 5,513632 4,208249 \n",
"A1CF 2,876904 3,078416 \n",
"A2M 3,288143 3,035124 \n",
"A2ML1 3,941870 2,782538 \n",
"A3GALT2 3,009816 2,634662 \n",
"A4GALT 3,513538 3,166587 \n",
" 5500994157493061613625_A05 5500994157493061613625_A06\n",
"A1BG 3,402282 4,914035 \n",
"A1CF 2,859689 3,226181 \n",
"A2M 3,266711 6,878105 \n",
"A2ML1 2,716182 2,912234 \n",
"A3GALT2 2,697715 2,593990 \n",
"A4GALT 3,240146 3,246475 \n",
" 5500994157493061613625_A07 5500994157493061613625_A08\n",
"A1BG 3,827411 5,147878 \n",
"A1CF 3,002562 2,899220 \n",
"A2M 3,306808 3,376042 \n",
"A2ML1 2,791071 2,829216 \n",
"A3GALT2 2,929163 2,744387 \n",
"A4GALT 3,801788 3,377124 \n",
" 5500994157493061613625_A09 5500994157493061613625_A10 ⋯\n",
"A1BG 3,110751 5,054884 ⋯\n",
"A1CF 2,761808 2,991242 ⋯\n",
"A2M 3,326467 3,532250 ⋯\n",
"A2ML1 2,736346 2,977346 ⋯\n",
"A3GALT2 2,998624 3,043765 ⋯\n",
"A4GALT 3,288002 3,361292 ⋯\n",
" 5500994175999120813240_H02 5500994175999120813240_H03\n",
"A1BG 4,273165 3,442682 \n",
"A1CF 2,948285 3,162107 \n",
"A2M 3,898669 3,478617 \n",
"A2ML1 2,904620 2,795384 \n",
"A3GALT2 2,964269 3,067023 \n",
"A4GALT 3,384112 3,070601 \n",
" 5500994175999120813240_H04 5500994175999120813240_H05\n",
"A1BG 4,923977 2,901377 \n",
"A1CF 2,989301 3,122200 \n",
"A2M 3,251410 6,346759 \n",
"A2ML1 2,714010 2,835382 \n",
"A3GALT2 2,768809 2,607127 \n",
"A4GALT 2,986975 3,334498 \n",
" 5500994175999120813240_H06 5500994175999120813240_H07\n",
"A1BG 4,528475 5,079415 \n",
"A1CF 2,981742 2,912033 \n",
"A2M 3,532383 3,161646 \n",
"A2ML1 2,763315 2,752095 \n",
"A3GALT2 2,778964 2,850118 \n",
"A4GALT 3,398661 3,195717 \n",
" 5500994175999120813240_H08 5500994175999120813240_H09\n",
"A1BG 2,959578 3,094308 \n",
"A1CF 2,950125 2,788239 \n",
"A2M 3,203922 3,483303 \n",
"A2ML1 2,911493 2,920386 \n",
"A3GALT2 2,703913 2,663925 \n",
"A4GALT 3,277447 4,407162 \n",
" 5500994175999120813240_H10 5500994175999120813240_H11\n",
"A1BG 4,045297 5,339831 \n",
"A1CF 2,874734 2,930411 \n",
"A2M 5,147751 8,860099 \n",
"A2ML1 2,794910 2,991144 \n",
"A3GALT2 2,763491 2,604637 \n",
"A4GALT 3,008970 3,053538 "
]
},
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{
"data": {
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"934"
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"934"
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"934"
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"[1] 934"
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"<table>\n",
"<thead><tr><th></th><th scope=col>Assay.Name</th><th scope=col>Characteristics.cell.line.</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><th scope=row>5500994157493061613625_A01</th><td>5500994157493061613625_A01</td><td>CAL.120 </td></tr>\n",
"\t<tr><th scope=row>5500994157493061613625_A02</th><td>5500994157493061613625_A02</td><td>DMS.114 </td></tr>\n",
"\t<tr><th scope=row>5500994157493061613625_A03</th><td>5500994157493061613625_A03</td><td>CAL.51 </td></tr>\n",
"\t<tr><th scope=row>5500994157493061613625_A04</th><td>5500994157493061613625_A04</td><td>H2869 </td></tr>\n",
"\t<tr><th scope=row>5500994157493061613625_A05</th><td>5500994157493061613625_A05</td><td>H290 </td></tr>\n",
"\t<tr><th scope=row>5500994157493061613625_A06</th><td>5500994157493061613625_A06</td><td>A2058 </td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|ll}\n",
" & Assay.Name & Characteristics.cell.line.\\\\\n",
"\\hline\n",
"\t5500994157493061613625\\_A01 & 5500994157493061613625\\_A01 & CAL.120 \\\\\n",
"\t5500994157493061613625\\_A02 & 5500994157493061613625\\_A02 & DMS.114 \\\\\n",
"\t5500994157493061613625\\_A03 & 5500994157493061613625\\_A03 & CAL.51 \\\\\n",
"\t5500994157493061613625\\_A04 & 5500994157493061613625\\_A04 & H2869 \\\\\n",
"\t5500994157493061613625\\_A05 & 5500994157493061613625\\_A05 & H290 \\\\\n",
"\t5500994157493061613625\\_A06 & 5500994157493061613625\\_A06 & A2058 \\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"| <!--/--> | Assay.Name | Characteristics.cell.line. | \n",
"|---|---|---|---|---|---|\n",
"| 5500994157493061613625_A01 | 5500994157493061613625_A01 | CAL.120 | \n",
"| 5500994157493061613625_A02 | 5500994157493061613625_A02 | DMS.114 | \n",
"| 5500994157493061613625_A03 | 5500994157493061613625_A03 | CAL.51 | \n",
"| 5500994157493061613625_A04 | 5500994157493061613625_A04 | H2869 | \n",
"| 5500994157493061613625_A05 | 5500994157493061613625_A05 | H290 | \n",
"| 5500994157493061613625_A06 | 5500994157493061613625_A06 | A2058 | \n",
"\n",
"\n"
],
"text/plain": [
" Assay.Name \n",
"5500994157493061613625_A01 5500994157493061613625_A01\n",
"5500994157493061613625_A02 5500994157493061613625_A02\n",
"5500994157493061613625_A03 5500994157493061613625_A03\n",
"5500994157493061613625_A04 5500994157493061613625_A04\n",
"5500994157493061613625_A05 5500994157493061613625_A05\n",
"5500994157493061613625_A06 5500994157493061613625_A06\n",
" Characteristics.cell.line.\n",
"5500994157493061613625_A01 CAL.120 \n",
"5500994157493061613625_A02 DMS.114 \n",
"5500994157493061613625_A03 CAL.51 \n",
"5500994157493061613625_A04 H2869 \n",
"5500994157493061613625_A05 H290 \n",
"5500994157493061613625_A06 A2058 "
]
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"<table>\n",
"<thead><tr><th></th><th scope=col>Assay.Name</th><th scope=col>Characteristics.cell.line.</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><th scope=row>5500994175999120813240_H05</th><td>5500994175999120813240_H05</td><td>MOG.G.UVW </td></tr>\n",
"\t<tr><th scope=row>5500994175999120813240_H06</th><td>5500994175999120813240_H06</td><td>MET.2B </td></tr>\n",
"\t<tr><th scope=row>5500994175999120813240_H07</th><td>5500994175999120813240_H07</td><td>JIMT.1 </td></tr>\n",
"\t<tr><th scope=row>5500994175999120813240_H08</th><td>5500994175999120813240_H08</td><td>PEO1 </td></tr>\n",
"\t<tr><th scope=row>5500994175999120813240_H09</th><td>5500994175999120813240_H09</td><td>PL4 </td></tr>\n",
"\t<tr><th scope=row>5500994175999120813240_H10</th><td>5500994175999120813240_H10</td><td>TT </td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|ll}\n",
" & Assay.Name & Characteristics.cell.line.\\\\\n",
"\\hline\n",
"\t5500994175999120813240\\_H05 & 5500994175999120813240\\_H05 & MOG.G.UVW \\\\\n",
"\t5500994175999120813240\\_H06 & 5500994175999120813240\\_H06 & MET.2B \\\\\n",
"\t5500994175999120813240\\_H07 & 5500994175999120813240\\_H07 & JIMT.1 \\\\\n",
"\t5500994175999120813240\\_H08 & 5500994175999120813240\\_H08 & PEO1 \\\\\n",
"\t5500994175999120813240\\_H09 & 5500994175999120813240\\_H09 & PL4 \\\\\n",
"\t5500994175999120813240\\_H10 & 5500994175999120813240\\_H10 & TT \\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"| <!--/--> | Assay.Name | Characteristics.cell.line. | \n",
"|---|---|---|---|---|---|\n",
"| 5500994175999120813240_H05 | 5500994175999120813240_H05 | MOG.G.UVW | \n",
"| 5500994175999120813240_H06 | 5500994175999120813240_H06 | MET.2B | \n",
"| 5500994175999120813240_H07 | 5500994175999120813240_H07 | JIMT.1 | \n",
"| 5500994175999120813240_H08 | 5500994175999120813240_H08 | PEO1 | \n",
"| 5500994175999120813240_H09 | 5500994175999120813240_H09 | PL4 | \n",
"| 5500994175999120813240_H10 | 5500994175999120813240_H10 | TT | \n",
"\n",
"\n"
],
"text/plain": [
" Assay.Name \n",
"5500994175999120813240_H05 5500994175999120813240_H05\n",
"5500994175999120813240_H06 5500994175999120813240_H06\n",
"5500994175999120813240_H07 5500994175999120813240_H07\n",
"5500994175999120813240_H08 5500994175999120813240_H08\n",
"5500994175999120813240_H09 5500994175999120813240_H09\n",
"5500994175999120813240_H10 5500994175999120813240_H10\n",
" Characteristics.cell.line.\n",
"5500994175999120813240_H05 MOG.G.UVW \n",
"5500994175999120813240_H06 MET.2B \n",
"5500994175999120813240_H07 JIMT.1 \n",
"5500994175999120813240_H08 PEO1 \n",
"5500994175999120813240_H09 PL4 \n",
"5500994175999120813240_H10 TT "
]
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"text/html": [
"<table>\n",
"<thead><tr><th></th><th scope=col>5500994157493061613625_A01</th><th scope=col>5500994157493061613625_A02</th><th scope=col>5500994157493061613625_A03</th><th scope=col>5500994157493061613625_A04</th><th scope=col>5500994157493061613625_A05</th><th scope=col>5500994157493061613625_A06</th><th scope=col>5500994157493061613625_A07</th><th scope=col>5500994157493061613625_A08</th><th scope=col>5500994157493061613625_A09</th><th scope=col>5500994157493061613625_A10</th><th scope=col>⋯</th><th scope=col>5500994175999120813240_H01</th><th scope=col>5500994175999120813240_H02</th><th scope=col>5500994175999120813240_H03</th><th scope=col>5500994175999120813240_H04</th><th scope=col>5500994175999120813240_H05</th><th scope=col>5500994175999120813240_H06</th><th scope=col>5500994175999120813240_H07</th><th scope=col>5500994175999120813240_H08</th><th scope=col>5500994175999120813240_H09</th><th scope=col>5500994175999120813240_H10</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><th scope=row>A1BG</th><td>6,210671</td><td>5,029226</td><td>5,513632</td><td>4,208249</td><td>3,402282</td><td>4,914035</td><td>3,827411</td><td>5,147878</td><td>3,110751</td><td>5,054884</td><td>⋯ </td><td>3,853365</td><td>4,273165</td><td>3,442682</td><td>4,923977</td><td>2,901377</td><td>4,528475</td><td>5,079415</td><td>2,959578</td><td>3,094308</td><td>4,045297</td></tr>\n",
"\t<tr><th scope=row>A1CF</th><td>2,986196</td><td>2,952698</td><td>2,876904</td><td>3,078416</td><td>2,859689</td><td>3,226181</td><td>3,002562</td><td>2,899220</td><td>2,761808</td><td>2,991242</td><td>⋯ </td><td>7,746021</td><td>2,948285</td><td>3,162107</td><td>2,989301</td><td>3,122200</td><td>2,981742</td><td>2,912033</td><td>2,950125</td><td>2,788239</td><td>2,874734</td></tr>\n",
"\t<tr><th scope=row>A2M</th><td>3,138822</td><td>3,339745</td><td>3,288143</td><td>3,035124</td><td>3,266711</td><td>6,878105</td><td>3,306808</td><td>3,376042</td><td>3,326467</td><td>3,532250</td><td>⋯ </td><td>3,801339</td><td>3,898669</td><td>3,478617</td><td>3,251410</td><td>6,346759</td><td>3,532383</td><td>3,161646</td><td>3,203922</td><td>3,483303</td><td>5,147751</td></tr>\n",
"\t<tr><th scope=row>A2ML1</th><td>2,659014</td><td>2,740146</td><td>3,941870</td><td>2,782538</td><td>2,716182</td><td>2,912234</td><td>2,791071</td><td>2,829216</td><td>2,736346</td><td>2,977346</td><td>⋯ </td><td>2,788015</td><td>2,904620</td><td>2,795384</td><td>2,714010</td><td>2,835382</td><td>2,763315</td><td>2,752095</td><td>2,911493</td><td>2,920386</td><td>2,794910</td></tr>\n",
"\t<tr><th scope=row>A3GALT2</th><td>2,765093</td><td>2,871171</td><td>3,009816</td><td>2,634662</td><td>2,697715</td><td>2,593990</td><td>2,929163</td><td>2,744387</td><td>2,998624</td><td>3,043765</td><td>⋯ </td><td>2,579725</td><td>2,964269</td><td>3,067023</td><td>2,768809</td><td>2,607127</td><td>2,778964</td><td>2,850118</td><td>2,703913</td><td>2,663925</td><td>2,763491</td></tr>\n",
"\t<tr><th scope=row>A4GALT</th><td>3,342432</td><td>3,138229</td><td>3,513538</td><td>3,166587</td><td>3,240146</td><td>3,246475</td><td>3,801788</td><td>3,377124</td><td>3,288002</td><td>3,361292</td><td>⋯ </td><td>3,378919</td><td>3,384112</td><td>3,070601</td><td>2,986975</td><td>3,334498</td><td>3,398661</td><td>3,195717</td><td>3,277447</td><td>4,407162</td><td>3,008970</td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|llllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllll}\n",
" & 5500994157493061613625\\_A01 & 5500994157493061613625\\_A02 & 5500994157493061613625\\_A03 & 5500994157493061613625\\_A04 & 5500994157493061613625\\_A05 & 5500994157493061613625\\_A06 & 5500994157493061613625\\_A07 & 5500994157493061613625\\_A08 & 5500994157493061613625\\_A09 & 5500994157493061613625\\_A10 & ⋯ & 5500994175999120813240\\_H01 & 5500994175999120813240\\_H02 & 5500994175999120813240\\_H03 & 5500994175999120813240\\_H04 & 5500994175999120813240\\_H05 & 5500994175999120813240\\_H06 & 5500994175999120813240\\_H07 & 5500994175999120813240\\_H08 & 5500994175999120813240\\_H09 & 5500994175999120813240\\_H10\\\\\n",
"\\hline\n",
"\tA1BG & 6,210671 & 5,029226 & 5,513632 & 4,208249 & 3,402282 & 4,914035 & 3,827411 & 5,147878 & 3,110751 & 5,054884 & ⋯ & 3,853365 & 4,273165 & 3,442682 & 4,923977 & 2,901377 & 4,528475 & 5,079415 & 2,959578 & 3,094308 & 4,045297\\\\\n",
"\tA1CF & 2,986196 & 2,952698 & 2,876904 & 3,078416 & 2,859689 & 3,226181 & 3,002562 & 2,899220 & 2,761808 & 2,991242 & ⋯ & 7,746021 & 2,948285 & 3,162107 & 2,989301 & 3,122200 & 2,981742 & 2,912033 & 2,950125 & 2,788239 & 2,874734\\\\\n",
"\tA2M & 3,138822 & 3,339745 & 3,288143 & 3,035124 & 3,266711 & 6,878105 & 3,306808 & 3,376042 & 3,326467 & 3,532250 & ⋯ & 3,801339 & 3,898669 & 3,478617 & 3,251410 & 6,346759 & 3,532383 & 3,161646 & 3,203922 & 3,483303 & 5,147751\\\\\n",
"\tA2ML1 & 2,659014 & 2,740146 & 3,941870 & 2,782538 & 2,716182 & 2,912234 & 2,791071 & 2,829216 & 2,736346 & 2,977346 & ⋯ & 2,788015 & 2,904620 & 2,795384 & 2,714010 & 2,835382 & 2,763315 & 2,752095 & 2,911493 & 2,920386 & 2,794910\\\\\n",
"\tA3GALT2 & 2,765093 & 2,871171 & 3,009816 & 2,634662 & 2,697715 & 2,593990 & 2,929163 & 2,744387 & 2,998624 & 3,043765 & ⋯ & 2,579725 & 2,964269 & 3,067023 & 2,768809 & 2,607127 & 2,778964 & 2,850118 & 2,703913 & 2,663925 & 2,763491\\\\\n",
"\tA4GALT & 3,342432 & 3,138229 & 3,513538 & 3,166587 & 3,240146 & 3,246475 & 3,801788 & 3,377124 & 3,288002 & 3,361292 & ⋯ & 3,378919 & 3,384112 & 3,070601 & 2,986975 & 3,334498 & 3,398661 & 3,195717 & 3,277447 & 4,407162 & 3,008970\\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"| <!--/--> | 5500994157493061613625_A01 | 5500994157493061613625_A02 | 5500994157493061613625_A03 | 5500994157493061613625_A04 | 5500994157493061613625_A05 | 5500994157493061613625_A06 | 5500994157493061613625_A07 | 5500994157493061613625_A08 | 5500994157493061613625_A09 | 5500994157493061613625_A10 | ⋯ | 5500994175999120813240_H01 | 5500994175999120813240_H02 | 5500994175999120813240_H03 | 5500994175999120813240_H04 | 5500994175999120813240_H05 | 5500994175999120813240_H06 | 5500994175999120813240_H07 | 5500994175999120813240_H08 | 5500994175999120813240_H09 | 5500994175999120813240_H10 | \n",
"|---|---|---|---|---|---|\n",
"| A1BG | 6,210671 | 5,029226 | 5,513632 | 4,208249 | 3,402282 | 4,914035 | 3,827411 | 5,147878 | 3,110751 | 5,054884 | ⋯ | 3,853365 | 4,273165 | 3,442682 | 4,923977 | 2,901377 | 4,528475 | 5,079415 | 2,959578 | 3,094308 | 4,045297 | \n",
"| A1CF | 2,986196 | 2,952698 | 2,876904 | 3,078416 | 2,859689 | 3,226181 | 3,002562 | 2,899220 | 2,761808 | 2,991242 | ⋯ | 7,746021 | 2,948285 | 3,162107 | 2,989301 | 3,122200 | 2,981742 | 2,912033 | 2,950125 | 2,788239 | 2,874734 | \n",
"| A2M | 3,138822 | 3,339745 | 3,288143 | 3,035124 | 3,266711 | 6,878105 | 3,306808 | 3,376042 | 3,326467 | 3,532250 | ⋯ | 3,801339 | 3,898669 | 3,478617 | 3,251410 | 6,346759 | 3,532383 | 3,161646 | 3,203922 | 3,483303 | 5,147751 | \n",
"| A2ML1 | 2,659014 | 2,740146 | 3,941870 | 2,782538 | 2,716182 | 2,912234 | 2,791071 | 2,829216 | 2,736346 | 2,977346 | ⋯ | 2,788015 | 2,904620 | 2,795384 | 2,714010 | 2,835382 | 2,763315 | 2,752095 | 2,911493 | 2,920386 | 2,794910 | \n",
"| A3GALT2 | 2,765093 | 2,871171 | 3,009816 | 2,634662 | 2,697715 | 2,593990 | 2,929163 | 2,744387 | 2,998624 | 3,043765 | ⋯ | 2,579725 | 2,964269 | 3,067023 | 2,768809 | 2,607127 | 2,778964 | 2,850118 | 2,703913 | 2,663925 | 2,763491 | \n",
"| A4GALT | 3,342432 | 3,138229 | 3,513538 | 3,166587 | 3,240146 | 3,246475 | 3,801788 | 3,377124 | 3,288002 | 3,361292 | ⋯ | 3,378919 | 3,384112 | 3,070601 | 2,986975 | 3,334498 | 3,398661 | 3,195717 | 3,277447 | 4,407162 | 3,008970 | \n",
"\n",
"\n"
],
"text/plain": [
" 5500994157493061613625_A01 5500994157493061613625_A02\n",
"A1BG 6,210671 5,029226 \n",
"A1CF 2,986196 2,952698 \n",
"A2M 3,138822 3,339745 \n",
"A2ML1 2,659014 2,740146 \n",
"A3GALT2 2,765093 2,871171 \n",
"A4GALT 3,342432 3,138229 \n",
" 5500994157493061613625_A03 5500994157493061613625_A04\n",
"A1BG 5,513632 4,208249 \n",
"A1CF 2,876904 3,078416 \n",
"A2M 3,288143 3,035124 \n",
"A2ML1 3,941870 2,782538 \n",
"A3GALT2 3,009816 2,634662 \n",
"A4GALT 3,513538 3,166587 \n",
" 5500994157493061613625_A05 5500994157493061613625_A06\n",
"A1BG 3,402282 4,914035 \n",
"A1CF 2,859689 3,226181 \n",
"A2M 3,266711 6,878105 \n",
"A2ML1 2,716182 2,912234 \n",
"A3GALT2 2,697715 2,593990 \n",
"A4GALT 3,240146 3,246475 \n",
" 5500994157493061613625_A07 5500994157493061613625_A08\n",
"A1BG 3,827411 5,147878 \n",
"A1CF 3,002562 2,899220 \n",
"A2M 3,306808 3,376042 \n",
"A2ML1 2,791071 2,829216 \n",
"A3GALT2 2,929163 2,744387 \n",
"A4GALT 3,801788 3,377124 \n",
" 5500994157493061613625_A09 5500994157493061613625_A10 ⋯\n",
"A1BG 3,110751 5,054884 ⋯\n",
"A1CF 2,761808 2,991242 ⋯\n",
"A2M 3,326467 3,532250 ⋯\n",
"A2ML1 2,736346 2,977346 ⋯\n",
"A3GALT2 2,998624 3,043765 ⋯\n",
"A4GALT 3,288002 3,361292 ⋯\n",
" 5500994175999120813240_H01 5500994175999120813240_H02\n",
"A1BG 3,853365 4,273165 \n",
"A1CF 7,746021 2,948285 \n",
"A2M 3,801339 3,898669 \n",
"A2ML1 2,788015 2,904620 \n",
"A3GALT2 2,579725 2,964269 \n",
"A4GALT 3,378919 3,384112 \n",
" 5500994175999120813240_H03 5500994175999120813240_H04\n",
"A1BG 3,442682 4,923977 \n",
"A1CF 3,162107 2,989301 \n",
"A2M 3,478617 3,251410 \n",
"A2ML1 2,795384 2,714010 \n",
"A3GALT2 3,067023 2,768809 \n",
"A4GALT 3,070601 2,986975 \n",
" 5500994175999120813240_H05 5500994175999120813240_H06\n",
"A1BG 2,901377 4,528475 \n",
"A1CF 3,122200 2,981742 \n",
"A2M 6,346759 3,532383 \n",
"A2ML1 2,835382 2,763315 \n",
"A3GALT2 2,607127 2,778964 \n",
"A4GALT 3,334498 3,398661 \n",
" 5500994175999120813240_H07 5500994175999120813240_H08\n",
"A1BG 5,079415 2,959578 \n",
"A1CF 2,912033 2,950125 \n",
"A2M 3,161646 3,203922 \n",
"A2ML1 2,752095 2,911493 \n",
"A3GALT2 2,850118 2,703913 \n",
"A4GALT 3,195717 3,277447 \n",
" 5500994175999120813240_H09 5500994175999120813240_H10\n",
"A1BG 3,094308 4,045297 \n",
"A1CF 2,788239 2,874734 \n",
"A2M 3,483303 5,147751 \n",
"A2ML1 2,920386 2,794910 \n",
"A3GALT2 2,663925 2,763491 \n",
"A4GALT 4,407162 3,008970 "
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th></th><th scope=col>CAL.120</th><th scope=col>DMS.114</th><th scope=col>CAL.51</th><th scope=col>H2869</th><th scope=col>H290</th><th scope=col>A2058</th><th scope=col>CESS</th><th scope=col>H2803</th><th scope=col>H2722</th><th scope=col>HCC1419</th><th scope=col>⋯</th><th scope=col>NCI.H716</th><th scope=col>LB831.BLC</th><th scope=col>HC.1</th><th scope=col>JURKAT</th><th scope=col>MOG.G.UVW</th><th scope=col>MET.2B</th><th scope=col>JIMT.1</th><th scope=col>PEO1</th><th scope=col>PL4</th><th scope=col>TT</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><th scope=row>A1BG</th><td>6,210671</td><td>5,029226</td><td>5,513632</td><td>4,208249</td><td>3,402282</td><td>4,914035</td><td>3,827411</td><td>5,147878</td><td>3,110751</td><td>5,054884</td><td>⋯ </td><td>3,853365</td><td>4,273165</td><td>3,442682</td><td>4,923977</td><td>2,901377</td><td>4,528475</td><td>5,079415</td><td>2,959578</td><td>3,094308</td><td>4,045297</td></tr>\n",
"\t<tr><th scope=row>A1CF</th><td>2,986196</td><td>2,952698</td><td>2,876904</td><td>3,078416</td><td>2,859689</td><td>3,226181</td><td>3,002562</td><td>2,899220</td><td>2,761808</td><td>2,991242</td><td>⋯ </td><td>7,746021</td><td>2,948285</td><td>3,162107</td><td>2,989301</td><td>3,122200</td><td>2,981742</td><td>2,912033</td><td>2,950125</td><td>2,788239</td><td>2,874734</td></tr>\n",
"\t<tr><th scope=row>A2M</th><td>3,138822</td><td>3,339745</td><td>3,288143</td><td>3,035124</td><td>3,266711</td><td>6,878105</td><td>3,306808</td><td>3,376042</td><td>3,326467</td><td>3,532250</td><td>⋯ </td><td>3,801339</td><td>3,898669</td><td>3,478617</td><td>3,251410</td><td>6,346759</td><td>3,532383</td><td>3,161646</td><td>3,203922</td><td>3,483303</td><td>5,147751</td></tr>\n",
"\t<tr><th scope=row>A2ML1</th><td>2,659014</td><td>2,740146</td><td>3,941870</td><td>2,782538</td><td>2,716182</td><td>2,912234</td><td>2,791071</td><td>2,829216</td><td>2,736346</td><td>2,977346</td><td>⋯ </td><td>2,788015</td><td>2,904620</td><td>2,795384</td><td>2,714010</td><td>2,835382</td><td>2,763315</td><td>2,752095</td><td>2,911493</td><td>2,920386</td><td>2,794910</td></tr>\n",
"\t<tr><th scope=row>A3GALT2</th><td>2,765093</td><td>2,871171</td><td>3,009816</td><td>2,634662</td><td>2,697715</td><td>2,593990</td><td>2,929163</td><td>2,744387</td><td>2,998624</td><td>3,043765</td><td>⋯ </td><td>2,579725</td><td>2,964269</td><td>3,067023</td><td>2,768809</td><td>2,607127</td><td>2,778964</td><td>2,850118</td><td>2,703913</td><td>2,663925</td><td>2,763491</td></tr>\n",
"\t<tr><th scope=row>A4GALT</th><td>3,342432</td><td>3,138229</td><td>3,513538</td><td>3,166587</td><td>3,240146</td><td>3,246475</td><td>3,801788</td><td>3,377124</td><td>3,288002</td><td>3,361292</td><td>⋯ </td><td>3,378919</td><td>3,384112</td><td>3,070601</td><td>2,986975</td><td>3,334498</td><td>3,398661</td><td>3,195717</td><td>3,277447</td><td>4,407162</td><td>3,008970</td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|llllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllll}\n",
" & CAL.120 & DMS.114 & CAL.51 & H2869 & H290 & A2058 & CESS & H2803 & H2722 & HCC1419 & ⋯ & NCI.H716 & LB831.BLC & HC.1 & JURKAT & MOG.G.UVW & MET.2B & JIMT.1 & PEO1 & PL4 & TT\\\\\n",
"\\hline\n",
"\tA1BG & 6,210671 & 5,029226 & 5,513632 & 4,208249 & 3,402282 & 4,914035 & 3,827411 & 5,147878 & 3,110751 & 5,054884 & ⋯ & 3,853365 & 4,273165 & 3,442682 & 4,923977 & 2,901377 & 4,528475 & 5,079415 & 2,959578 & 3,094308 & 4,045297\\\\\n",
"\tA1CF & 2,986196 & 2,952698 & 2,876904 & 3,078416 & 2,859689 & 3,226181 & 3,002562 & 2,899220 & 2,761808 & 2,991242 & ⋯ & 7,746021 & 2,948285 & 3,162107 & 2,989301 & 3,122200 & 2,981742 & 2,912033 & 2,950125 & 2,788239 & 2,874734\\\\\n",
"\tA2M & 3,138822 & 3,339745 & 3,288143 & 3,035124 & 3,266711 & 6,878105 & 3,306808 & 3,376042 & 3,326467 & 3,532250 & ⋯ & 3,801339 & 3,898669 & 3,478617 & 3,251410 & 6,346759 & 3,532383 & 3,161646 & 3,203922 & 3,483303 & 5,147751\\\\\n",
"\tA2ML1 & 2,659014 & 2,740146 & 3,941870 & 2,782538 & 2,716182 & 2,912234 & 2,791071 & 2,829216 & 2,736346 & 2,977346 & ⋯ & 2,788015 & 2,904620 & 2,795384 & 2,714010 & 2,835382 & 2,763315 & 2,752095 & 2,911493 & 2,920386 & 2,794910\\\\\n",
"\tA3GALT2 & 2,765093 & 2,871171 & 3,009816 & 2,634662 & 2,697715 & 2,593990 & 2,929163 & 2,744387 & 2,998624 & 3,043765 & ⋯ & 2,579725 & 2,964269 & 3,067023 & 2,768809 & 2,607127 & 2,778964 & 2,850118 & 2,703913 & 2,663925 & 2,763491\\\\\n",
"\tA4GALT & 3,342432 & 3,138229 & 3,513538 & 3,166587 & 3,240146 & 3,246475 & 3,801788 & 3,377124 & 3,288002 & 3,361292 & ⋯ & 3,378919 & 3,384112 & 3,070601 & 2,986975 & 3,334498 & 3,398661 & 3,195717 & 3,277447 & 4,407162 & 3,008970\\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"| <!--/--> | CAL.120 | DMS.114 | CAL.51 | H2869 | H290 | A2058 | CESS | H2803 | H2722 | HCC1419 | ⋯ | NCI.H716 | LB831.BLC | HC.1 | JURKAT | MOG.G.UVW | MET.2B | JIMT.1 | PEO1 | PL4 | TT | \n",
"|---|---|---|---|---|---|\n",
"| A1BG | 6,210671 | 5,029226 | 5,513632 | 4,208249 | 3,402282 | 4,914035 | 3,827411 | 5,147878 | 3,110751 | 5,054884 | ⋯ | 3,853365 | 4,273165 | 3,442682 | 4,923977 | 2,901377 | 4,528475 | 5,079415 | 2,959578 | 3,094308 | 4,045297 | \n",
"| A1CF | 2,986196 | 2,952698 | 2,876904 | 3,078416 | 2,859689 | 3,226181 | 3,002562 | 2,899220 | 2,761808 | 2,991242 | ⋯ | 7,746021 | 2,948285 | 3,162107 | 2,989301 | 3,122200 | 2,981742 | 2,912033 | 2,950125 | 2,788239 | 2,874734 | \n",
"| A2M | 3,138822 | 3,339745 | 3,288143 | 3,035124 | 3,266711 | 6,878105 | 3,306808 | 3,376042 | 3,326467 | 3,532250 | ⋯ | 3,801339 | 3,898669 | 3,478617 | 3,251410 | 6,346759 | 3,532383 | 3,161646 | 3,203922 | 3,483303 | 5,147751 | \n",
"| A2ML1 | 2,659014 | 2,740146 | 3,941870 | 2,782538 | 2,716182 | 2,912234 | 2,791071 | 2,829216 | 2,736346 | 2,977346 | ⋯ | 2,788015 | 2,904620 | 2,795384 | 2,714010 | 2,835382 | 2,763315 | 2,752095 | 2,911493 | 2,920386 | 2,794910 | \n",
"| A3GALT2 | 2,765093 | 2,871171 | 3,009816 | 2,634662 | 2,697715 | 2,593990 | 2,929163 | 2,744387 | 2,998624 | 3,043765 | ⋯ | 2,579725 | 2,964269 | 3,067023 | 2,768809 | 2,607127 | 2,778964 | 2,850118 | 2,703913 | 2,663925 | 2,763491 | \n",
"| A4GALT | 3,342432 | 3,138229 | 3,513538 | 3,166587 | 3,240146 | 3,246475 | 3,801788 | 3,377124 | 3,288002 | 3,361292 | ⋯ | 3,378919 | 3,384112 | 3,070601 | 2,986975 | 3,334498 | 3,398661 | 3,195717 | 3,277447 | 4,407162 | 3,008970 | \n",
"\n",
"\n"
],
"text/plain": [
" CAL.120 DMS.114 CAL.51 H2869 H290 A2058 CESS H2803 \n",
"A1BG 6,210671 5,029226 5,513632 4,208249 3,402282 4,914035 3,827411 5,147878\n",
"A1CF 2,986196 2,952698 2,876904 3,078416 2,859689 3,226181 3,002562 2,899220\n",
"A2M 3,138822 3,339745 3,288143 3,035124 3,266711 6,878105 3,306808 3,376042\n",
"A2ML1 2,659014 2,740146 3,941870 2,782538 2,716182 2,912234 2,791071 2,829216\n",
"A3GALT2 2,765093 2,871171 3,009816 2,634662 2,697715 2,593990 2,929163 2,744387\n",
"A4GALT 3,342432 3,138229 3,513538 3,166587 3,240146 3,246475 3,801788 3,377124\n",
" H2722 HCC1419 ⋯ NCI.H716 LB831.BLC HC.1 JURKAT MOG.G.UVW\n",
"A1BG 3,110751 5,054884 ⋯ 3,853365 4,273165 3,442682 4,923977 2,901377 \n",
"A1CF 2,761808 2,991242 ⋯ 7,746021 2,948285 3,162107 2,989301 3,122200 \n",
"A2M 3,326467 3,532250 ⋯ 3,801339 3,898669 3,478617 3,251410 6,346759 \n",
"A2ML1 2,736346 2,977346 ⋯ 2,788015 2,904620 2,795384 2,714010 2,835382 \n",
"A3GALT2 2,998624 3,043765 ⋯ 2,579725 2,964269 3,067023 2,768809 2,607127 \n",
"A4GALT 3,288002 3,361292 ⋯ 3,378919 3,384112 3,070601 2,986975 3,334498 \n",
" MET.2B JIMT.1 PEO1 PL4 TT \n",
"A1BG 4,528475 5,079415 2,959578 3,094308 4,045297\n",
"A1CF 2,981742 2,912033 2,950125 2,788239 2,874734\n",
"A2M 3,532383 3,161646 3,203922 3,483303 5,147751\n",
"A2ML1 2,763315 2,752095 2,911493 2,920386 2,794910\n",
"A3GALT2 2,778964 2,850118 2,703913 2,663925 2,763491\n",
"A4GALT 3,398661 3,195717 3,277447 4,407162 3,008970"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"# rename columns in our data table\n",
"cl_names <- read.csv(\"GDSC/E-MTAB-3610.annotation.tsv\",header = T,sep=\"\\t\")\n",
"cl_names$Characteristics.cell.line. <- gsub(\"-\",\".\",cl_names$Characteristics.cell.line.)\n",
"cl_names <- cl_names[!cl_names$Characteristics.cell.line. %in% cl_names$Characteristics.cell.line.[duplicated(cl_names$Characteristics.cell.line. )],]\n",
"length(intersect(cl_names$Characteristics.cell.line.,colnames(GEX)))\n",
"row.names(cl_names) <- cl_names$Assay.Name\n",
"cl_names <- cl_names[colnames(exprs_GDSC_RMA_BrainArray_SYMBOL),]\n",
"cl_names <- cl_names[!is.na(cl_names$Assay.Name),]\n",
"\n",
"exprs_GDSC_RMA_BrainArray_SYMBOL_ <- exprs_GDSC_RMA_BrainArray_SYMBOL[,cl_names$Assay.Name]\n",
"colnames(exprs_GDSC_RMA_BrainArray_SYMBOL_) <- cl_names$Characteristics.cell.line.\n",
"head(exprs_GDSC_RMA_BrainArray_SYMBOL_)"
]
},
{
"cell_type": "code",
"execution_count": 68,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<span style=white-space:pre-wrap>'our data 18645'</span>"
],
"text/latex": [
"'our data 18645'"
],
"text/markdown": [
"<span style=white-space:pre-wrap>'our data 18645'</span>"
],
"text/plain": [
"[1] \"our data 18645\""
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"<span style=white-space:pre-wrap>'GEX 17419'</span>"
],
"text/latex": [
"'GEX 17419'"
],
"text/markdown": [
"<span style=white-space:pre-wrap>'GEX 17419'</span>"
],
"text/plain": [
"[1] \"GEX 17419\""
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"<span style=white-space:pre-wrap>'Intersection: Shared Genes 16639 Shared samples 934'</span>"
],
"text/latex": [
"'Intersection: Shared Genes 16639 Shared samples 934'"
],
"text/markdown": [
"<span style=white-space:pre-wrap>'Intersection: Shared Genes 16639 Shared samples 934'</span>"
],
"text/plain": [
"[1] \"Intersection: Shared Genes 16639 Shared samples 934\""
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"paste(\"our data\",dim(exprs_GDSC_RMA_BrainArray_SYMBOL_)[1], sep =\" \")\n",
"paste(\"GEX\",dim(GEX)[1], sep =\" \")\n",
"shared_genes <- intersect(row.names(GEX),row.names(exprs_GDSC_RMA_BrainArray_SYMBOL_))\n",
"shared_samples <- intersect(colnames(GEX),colnames(exprs_GDSC_RMA_BrainArray_SYMBOL_))\n",
"paste(\"Intersection: Shared Genes\",length(shared_genes),\"Shared samples\",length(shared_samples),sep=\" \")"
]
},
{
"cell_type": "code",
"execution_count": 69,
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"gene_corrs <- diag(cor(t(GEX[shared_genes,shared_samples]), t(exprs_GDSC_RMA_BrainArray_SYMBOL_[shared_genes,shared_samples])))\n",
"sample_corrs <- diag(cor(GEX[shared_genes,shared_samples], exprs_GDSC_RMA_BrainArray_SYMBOL_[shared_genes,shared_samples]))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Result:\n",
"* Correlation between samples is nearly perfect: 0.981-0.977, 0.98 on average;\n",
"* Gene profile correlation is also good for most genes (0.99 on average), but for some it is very poor: min. is -0.04"
]
},
{
"cell_type": "code",
"execution_count": 79,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<span style=white-space:pre-wrap>'Corr. between genes (mean, max, min) 0,987574861022879 0,999999501930154 -0,0466895425476415'</span>"
],
"text/latex": [
"'Corr. between genes (mean, max, min) 0,987574861022879 0,999999501930154 -0,0466895425476415'"
],
"text/markdown": [
"<span style=white-space:pre-wrap>'Corr. between genes (mean, max, min) 0,987574861022879 0,999999501930154 -0,0466895425476415'</span>"
],
"text/plain": [
"[1] \"Corr. between genes (mean, max, min) 0,987574861022879 0,999999501930154 -0,0466895425476415\""
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"<span style=white-space:pre-wrap>'Corr. between samples (mean, max, min) 0,97923761177824 0,980946265835985 0,977003232824752'</span>"
],
"text/latex": [
"'Corr. between samples (mean, max, min) 0,97923761177824 0,980946265835985 0,977003232824752'"
],
"text/markdown": [
"<span style=white-space:pre-wrap>'Corr. between samples (mean, max, min) 0,97923761177824 0,980946265835985 0,977003232824752'</span>"
],
"text/plain": [
"[1] \"Corr. between samples (mean, max, min) 0,97923761177824 0,980946265835985 0,977003232824752\""
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"# average correlation between genes \n",
"paste(\"Corr. between genes (mean, max, min)\",mean(gene_corrs),max(gene_corrs),min(gene_corrs), sep =\" \")\n",
"# average correlation between samples\n",
"paste(\"Corr. between samples (mean, max, min)\",mean(sample_corrs),max(sample_corrs),min(sample_corrs), sep =\" \")"
]
},
{
"cell_type": "code",
"execution_count": 80,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<dl class=dl-horizontal>\n",
"\t<dt>NDUFA13</dt>\n",
"\t\t<dd>-0,0466895425476415</dd>\n",
"\t<dt>AGRN</dt>\n",
"\t\t<dd>-0,0357717955240473</dd>\n",
"\t<dt>CCDC122</dt>\n",
"\t\t<dd>-0,00548321411413838</dd>\n",
"\t<dt>AKTIP</dt>\n",
"\t\t<dd>0,0184622017401918</dd>\n",
"\t<dt>TET3</dt>\n",
"\t\t<dd>0,0814979327351481</dd>\n",
"\t<dt>EXOSC7</dt>\n",
"\t\t<dd>0,0932529618544275</dd>\n",
"\t<dt>STARD10</dt>\n",
"\t\t<dd>0,118468067661345</dd>\n",
"\t<dt>NAA38</dt>\n",
"\t\t<dd>0,120170347929768</dd>\n",
"\t<dt>EFR3B</dt>\n",
"\t\t<dd>0,12613722046339</dd>\n",
"\t<dt>SPIN3</dt>\n",
"\t\t<dd>0,150719264107254</dd>\n",
"\t<dt>SMCR8</dt>\n",
"\t\t<dd>0,1582612418071</dd>\n",
"\t<dt>HS6ST3</dt>\n",
"\t\t<dd>0,196708977687097</dd>\n",
"\t<dt>OFCC1</dt>\n",
"\t\t<dd>0,213518347005132</dd>\n",
"\t<dt>RPL10</dt>\n",
"\t\t<dd>0,245640291331545</dd>\n",
"\t<dt>DLEU2</dt>\n",
"\t\t<dd>0,25076045963443</dd>\n",
"\t<dt>KLHL7</dt>\n",
"\t\t<dd>0,259364034605027</dd>\n",
"\t<dt>PPM1E</dt>\n",
"\t\t<dd>0,264811047564632</dd>\n",
"\t<dt>MKL2</dt>\n",
"\t\t<dd>0,268757227041272</dd>\n",
"\t<dt>DISC1</dt>\n",
"\t\t<dd>0,290808335661287</dd>\n",
"\t<dt>C3orf30</dt>\n",
"\t\t<dd>0,303613399674166</dd>\n",
"</dl>\n"
],
"text/latex": [
"\\begin{description*}\n",
"\\item[NDUFA13] -0,0466895425476415\n",
"\\item[AGRN] -0,0357717955240473\n",
"\\item[CCDC122] -0,00548321411413838\n",
"\\item[AKTIP] 0,0184622017401918\n",
"\\item[TET3] 0,0814979327351481\n",
"\\item[EXOSC7] 0,0932529618544275\n",
"\\item[STARD10] 0,118468067661345\n",
"\\item[NAA38] 0,120170347929768\n",
"\\item[EFR3B] 0,12613722046339\n",
"\\item[SPIN3] 0,150719264107254\n",
"\\item[SMCR8] 0,1582612418071\n",
"\\item[HS6ST3] 0,196708977687097\n",
"\\item[OFCC1] 0,213518347005132\n",
"\\item[RPL10] 0,245640291331545\n",
"\\item[DLEU2] 0,25076045963443\n",
"\\item[KLHL7] 0,259364034605027\n",
"\\item[PPM1E] 0,264811047564632\n",
"\\item[MKL2] 0,268757227041272\n",
"\\item[DISC1] 0,290808335661287\n",
"\\item[C3orf30] 0,303613399674166\n",
"\\end{description*}\n"
],
"text/markdown": [
"NDUFA13\n",
": -0,0466895425476415AGRN\n",
": -0,0357717955240473CCDC122\n",
": -0,00548321411413838AKTIP\n",
": 0,0184622017401918TET3\n",
": 0,0814979327351481EXOSC7\n",
": 0,0932529618544275STARD10\n",
": 0,118468067661345NAA38\n",
": 0,120170347929768EFR3B\n",
": 0,12613722046339SPIN3\n",
": 0,150719264107254SMCR8\n",
": 0,1582612418071HS6ST3\n",
": 0,196708977687097OFCC1\n",
": 0,213518347005132RPL10\n",
": 0,245640291331545DLEU2\n",
": 0,25076045963443KLHL7\n",
": 0,259364034605027PPM1E\n",
": 0,264811047564632MKL2\n",
": 0,268757227041272DISC1\n",
": 0,290808335661287C3orf30\n",
": 0,303613399674166\n",
"\n"
],
"text/plain": [
" NDUFA13 AGRN CCDC122 AKTIP TET3 EXOSC7 \n",
"-0,046689543 -0,035771796 -0,005483214 0,018462202 0,081497933 0,093252962 \n",
" STARD10 NAA38 EFR3B SPIN3 SMCR8 HS6ST3 \n",
" 0,118468068 0,120170348 0,126137220 0,150719264 0,158261242 0,196708978 \n",
" OFCC1 RPL10 DLEU2 KLHL7 PPM1E MKL2 \n",
" 0,213518347 0,245640291 0,250760460 0,259364035 0,264811048 0,268757227 \n",
" DISC1 C3orf30 \n",
" 0,290808336 0,303613400 "
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"# top 20 genes with the worst correlation \n",
"head(sort(gene_corrs,decreasing = FALSE),20)"
]
},
{
"cell_type": "code",
"execution_count": 81,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"587"
],
"text/latex": [
"587"
],
"text/markdown": [
"587"
],
"text/plain": [
"[1] 587"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"length(gene_corrs[gene_corrs<0.9])"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Compare expressions provided by Lukas Folkman with our results \n",
"\n",
"\n",
"### GSE6434\n",
"Resulted correlation of sample profiles for GSE6434"
]
},
{
"cell_type": "code",
"execution_count": 99,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Loading objects:\n",
" doceVivoNorm_syms\n",
" groupMembership\n"
]
}
],
"source": [
"load(\"Geeleher_with_GDSCr6/data/doce_rma_syms_brainArray.RData\",verbose = T)"
]
},
{
"cell_type": "code",
"execution_count": 100,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<ol class=list-inline>\n",
"\t<li>8399</li>\n",
"\t<li>24</li>\n",
"</ol>\n"
],
"text/latex": [
"\\begin{enumerate*}\n",
"\\item 8399\n",
"\\item 24\n",
"\\end{enumerate*}\n"
],
"text/markdown": [
"1. 8399\n",
"2. 24\n",
"\n",
"\n"
],
"text/plain": [
"[1] 8399 24"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th></th><th scope=col>GSM4903</th><th scope=col>GSM4907</th><th scope=col>GSM4908</th><th scope=col>GSM4914</th><th scope=col>GSM4915</th><th scope=col>GSM4917</th><th scope=col>GSM4919</th><th scope=col>GSM4920</th><th scope=col>GSM4921</th><th scope=col>GSM4923</th><th scope=col>⋯</th><th scope=col>GSM4906</th><th scope=col>GSM4909</th><th scope=col>GSM4910</th><th scope=col>GSM4911</th><th scope=col>GSM4912</th><th scope=col>GSM4913</th><th scope=col>GSM4916</th><th scope=col>GSM4918</th><th scope=col>GSM4922</th><th scope=col>GSM4924</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><th scope=row>AKT3</th><td>4,471063</td><td>4,624944</td><td>4,692121</td><td>4,466994</td><td>5,754121</td><td>4,554908</td><td>5,429423</td><td>4,312592</td><td>4,582778</td><td>4,528860</td><td>⋯ </td><td>4,815075</td><td>4,543328</td><td>4,204645</td><td>4,361776</td><td>5,068274</td><td>4,937692</td><td>4,759488</td><td>4,357240</td><td>4,177261</td><td>4,285073</td></tr>\n",
"\t<tr><th scope=row>MED6</th><td>3,839062</td><td>3,584472</td><td>3,326740</td><td>3,535239</td><td>3,742069</td><td>3,774019</td><td>3,677544</td><td>3,898045</td><td>3,855050</td><td>3,555893</td><td>⋯ </td><td>3,364237</td><td>3,667986</td><td>3,521200</td><td>3,502689</td><td>3,351606</td><td>3,525377</td><td>3,429070</td><td>3,956674</td><td>4,073611</td><td>3,682697</td></tr>\n",
"\t<tr><th scope=row>NR2E3</th><td>7,290057</td><td>7,399590</td><td>7,468425</td><td>7,677972</td><td>7,797163</td><td>8,160049</td><td>7,042885</td><td>7,989204</td><td>7,698802</td><td>7,518574</td><td>⋯ </td><td>7,511533</td><td>8,709372</td><td>8,222946</td><td>7,912787</td><td>7,671314</td><td>7,479153</td><td>8,212303</td><td>8,233507</td><td>7,851094</td><td>8,244293</td></tr>\n",
"\t<tr><th scope=row>NAALAD2</th><td>3,242835</td><td>3,710604</td><td>3,535582</td><td>4,681849</td><td>4,179551</td><td>3,944334</td><td>3,007184</td><td>4,539145</td><td>3,058529</td><td>4,224176</td><td>⋯ </td><td>4,132053</td><td>6,250989</td><td>4,565469</td><td>4,741568</td><td>3,704555</td><td>3,302500</td><td>4,680904</td><td>5,732379</td><td>4,786829</td><td>4,913436</td></tr>\n",
"\t<tr><th scope=row>NAALADL1</th><td>4,458982</td><td>4,539672</td><td>4,233429</td><td>4,309195</td><td>4,778892</td><td>4,536552</td><td>4,131638</td><td>4,760834</td><td>4,371971</td><td>4,365722</td><td>⋯ </td><td>4,455732</td><td>5,010709</td><td>4,587314</td><td>4,458041</td><td>4,298968</td><td>4,551020</td><td>4,380551</td><td>4,852454</td><td>4,650280</td><td>4,854401</td></tr>\n",
"\t<tr><th scope=row>ACOT8</th><td>5,100625</td><td>5,307493</td><td>5,405129</td><td>5,246431</td><td>5,714727</td><td>5,812253</td><td>5,115640</td><td>5,806674</td><td>5,922718</td><td>5,290012</td><td>⋯ </td><td>5,636612</td><td>6,111452</td><td>5,990468</td><td>5,492492</td><td>5,349489</td><td>5,440780</td><td>5,528125</td><td>5,955764</td><td>5,688114</td><td>5,585995</td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|llllllllllllllllllllllll}\n",
" & GSM4903 & GSM4907 & GSM4908 & GSM4914 & GSM4915 & GSM4917 & GSM4919 & GSM4920 & GSM4921 & GSM4923 & ⋯ & GSM4906 & GSM4909 & GSM4910 & GSM4911 & GSM4912 & GSM4913 & GSM4916 & GSM4918 & GSM4922 & GSM4924\\\\\n",
"\\hline\n",
"\tAKT3 & 4,471063 & 4,624944 & 4,692121 & 4,466994 & 5,754121 & 4,554908 & 5,429423 & 4,312592 & 4,582778 & 4,528860 & ⋯ & 4,815075 & 4,543328 & 4,204645 & 4,361776 & 5,068274 & 4,937692 & 4,759488 & 4,357240 & 4,177261 & 4,285073\\\\\n",
"\tMED6 & 3,839062 & 3,584472 & 3,326740 & 3,535239 & 3,742069 & 3,774019 & 3,677544 & 3,898045 & 3,855050 & 3,555893 & ⋯ & 3,364237 & 3,667986 & 3,521200 & 3,502689 & 3,351606 & 3,525377 & 3,429070 & 3,956674 & 4,073611 & 3,682697\\\\\n",
"\tNR2E3 & 7,290057 & 7,399590 & 7,468425 & 7,677972 & 7,797163 & 8,160049 & 7,042885 & 7,989204 & 7,698802 & 7,518574 & ⋯ & 7,511533 & 8,709372 & 8,222946 & 7,912787 & 7,671314 & 7,479153 & 8,212303 & 8,233507 & 7,851094 & 8,244293\\\\\n",
"\tNAALAD2 & 3,242835 & 3,710604 & 3,535582 & 4,681849 & 4,179551 & 3,944334 & 3,007184 & 4,539145 & 3,058529 & 4,224176 & ⋯ & 4,132053 & 6,250989 & 4,565469 & 4,741568 & 3,704555 & 3,302500 & 4,680904 & 5,732379 & 4,786829 & 4,913436\\\\\n",
"\tNAALADL1 & 4,458982 & 4,539672 & 4,233429 & 4,309195 & 4,778892 & 4,536552 & 4,131638 & 4,760834 & 4,371971 & 4,365722 & ⋯ & 4,455732 & 5,010709 & 4,587314 & 4,458041 & 4,298968 & 4,551020 & 4,380551 & 4,852454 & 4,650280 & 4,854401\\\\\n",
"\tACOT8 & 5,100625 & 5,307493 & 5,405129 & 5,246431 & 5,714727 & 5,812253 & 5,115640 & 5,806674 & 5,922718 & 5,290012 & ⋯ & 5,636612 & 6,111452 & 5,990468 & 5,492492 & 5,349489 & 5,440780 & 5,528125 & 5,955764 & 5,688114 & 5,585995\\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"| <!--/--> | GSM4903 | GSM4907 | GSM4908 | GSM4914 | GSM4915 | GSM4917 | GSM4919 | GSM4920 | GSM4921 | GSM4923 | ⋯ | GSM4906 | GSM4909 | GSM4910 | GSM4911 | GSM4912 | GSM4913 | GSM4916 | GSM4918 | GSM4922 | GSM4924 | \n",
"|---|---|---|---|---|---|\n",
"| AKT3 | 4,471063 | 4,624944 | 4,692121 | 4,466994 | 5,754121 | 4,554908 | 5,429423 | 4,312592 | 4,582778 | 4,528860 | ⋯ | 4,815075 | 4,543328 | 4,204645 | 4,361776 | 5,068274 | 4,937692 | 4,759488 | 4,357240 | 4,177261 | 4,285073 | \n",
"| MED6 | 3,839062 | 3,584472 | 3,326740 | 3,535239 | 3,742069 | 3,774019 | 3,677544 | 3,898045 | 3,855050 | 3,555893 | ⋯ | 3,364237 | 3,667986 | 3,521200 | 3,502689 | 3,351606 | 3,525377 | 3,429070 | 3,956674 | 4,073611 | 3,682697 | \n",
"| NR2E3 | 7,290057 | 7,399590 | 7,468425 | 7,677972 | 7,797163 | 8,160049 | 7,042885 | 7,989204 | 7,698802 | 7,518574 | ⋯ | 7,511533 | 8,709372 | 8,222946 | 7,912787 | 7,671314 | 7,479153 | 8,212303 | 8,233507 | 7,851094 | 8,244293 | \n",
"| NAALAD2 | 3,242835 | 3,710604 | 3,535582 | 4,681849 | 4,179551 | 3,944334 | 3,007184 | 4,539145 | 3,058529 | 4,224176 | ⋯ | 4,132053 | 6,250989 | 4,565469 | 4,741568 | 3,704555 | 3,302500 | 4,680904 | 5,732379 | 4,786829 | 4,913436 | \n",
"| NAALADL1 | 4,458982 | 4,539672 | 4,233429 | 4,309195 | 4,778892 | 4,536552 | 4,131638 | 4,760834 | 4,371971 | 4,365722 | ⋯ | 4,455732 | 5,010709 | 4,587314 | 4,458041 | 4,298968 | 4,551020 | 4,380551 | 4,852454 | 4,650280 | 4,854401 | \n",
"| ACOT8 | 5,100625 | 5,307493 | 5,405129 | 5,246431 | 5,714727 | 5,812253 | 5,115640 | 5,806674 | 5,922718 | 5,290012 | ⋯ | 5,636612 | 6,111452 | 5,990468 | 5,492492 | 5,349489 | 5,440780 | 5,528125 | 5,955764 | 5,688114 | 5,585995 | \n",
"\n",
"\n"
],
"text/plain": [
" GSM4903 GSM4907 GSM4908 GSM4914 GSM4915 GSM4917 GSM4919 \n",
"AKT3 4,471063 4,624944 4,692121 4,466994 5,754121 4,554908 5,429423\n",
"MED6 3,839062 3,584472 3,326740 3,535239 3,742069 3,774019 3,677544\n",
"NR2E3 7,290057 7,399590 7,468425 7,677972 7,797163 8,160049 7,042885\n",
"NAALAD2 3,242835 3,710604 3,535582 4,681849 4,179551 3,944334 3,007184\n",
"NAALADL1 4,458982 4,539672 4,233429 4,309195 4,778892 4,536552 4,131638\n",
"ACOT8 5,100625 5,307493 5,405129 5,246431 5,714727 5,812253 5,115640\n",
" GSM4920 GSM4921 GSM4923 ⋯ GSM4906 GSM4909 GSM4910 GSM4911 \n",
"AKT3 4,312592 4,582778 4,528860 ⋯ 4,815075 4,543328 4,204645 4,361776\n",
"MED6 3,898045 3,855050 3,555893 ⋯ 3,364237 3,667986 3,521200 3,502689\n",
"NR2E3 7,989204 7,698802 7,518574 ⋯ 7,511533 8,709372 8,222946 7,912787\n",
"NAALAD2 4,539145 3,058529 4,224176 ⋯ 4,132053 6,250989 4,565469 4,741568\n",
"NAALADL1 4,760834 4,371971 4,365722 ⋯ 4,455732 5,010709 4,587314 4,458041\n",
"ACOT8 5,806674 5,922718 5,290012 ⋯ 5,636612 6,111452 5,990468 5,492492\n",
" GSM4912 GSM4913 GSM4916 GSM4918 GSM4922 GSM4924 \n",
"AKT3 5,068274 4,937692 4,759488 4,357240 4,177261 4,285073\n",
"MED6 3,351606 3,525377 3,429070 3,956674 4,073611 3,682697\n",
"NR2E3 7,671314 7,479153 8,212303 8,233507 7,851094 8,244293\n",
"NAALAD2 3,704555 3,302500 4,680904 5,732379 4,786829 4,913436\n",
"NAALADL1 4,298968 4,551020 4,380551 4,852454 4,650280 4,854401\n",
"ACOT8 5,349489 5,440780 5,528125 5,955764 5,688114 5,585995"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"dim(doceVivoNorm_syms)\n",
"colnames(doceVivoNorm_syms) <- gsub(\".CEL\",\"\",colnames(doceVivoNorm_syms))\n",
"head(doceVivoNorm_syms)"
]
},
{
"cell_type": "code",
"execution_count": 83,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"24"
],
"text/latex": [
"24"
],
"text/markdown": [
"24"
],
"text/plain": [
"[1] 24"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"24"
],
"text/latex": [
"24"
],
"text/markdown": [
"24"
],
"text/plain": [
"[1] 24"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"'hgu95av2cdf'"
],
"text/latex": [
"'hgu95av2cdf'"
],
"text/markdown": [
"'hgu95av2cdf'"
],
"text/plain": [
"[1] \"hgu95av2cdf\""
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"cel_file_dir = \"arrays/GSE6434/\"\n",
"getSnames <- function(sname,ext=\".CEL.gz\"){\n",
" sname <- sub(ext, \"\", sname)\n",
" #sname <- strsplit(sname,split=\"_\")\n",
" sname <- unlist(sname)[1]\n",
" return(sname)\n",
"}\n",
"fnames <- list.files(cel_file_dir ,pattern = \".CEL.gz\")\n",
"snames <- lapply(fnames, getSnames)\n",
"snames <- unlist(snames)\n",
"length(snames)\n",
"length(fnames)\n",
"\n",
"\n",
"cdf_basenames <- unique(unlist(lapply(fnames,getCDFname, dir=cel_file_dir)))\n",
"cdf_basenames \n",
"\n",
"cdf_basename <- sub(\"cdf\",\"\",cdf_basenames[1])\n",
"\n",
"# load BrainArray\n",
"customAnno <- installBrainArrayCDFandDB(paste0(cdf_basename,\"hs\"),version='22.0.0',gene_id_type=\"entrezg\",\n",
" download_dir=\"/home/olya/SFU/Hossein/arrays/\")"
]
},
{
"cell_type": "code",
"execution_count": 86,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"'hgu95av2hsentrezgcdf'"
],
"text/latex": [
"'hgu95av2hsentrezgcdf'"
],
"text/markdown": [
"'hgu95av2hsentrezgcdf'"
],
"text/plain": [
"[1] \"hgu95av2hsentrezgcdf\""
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"<ol class=list-inline>\n",
"\t<li>8519</li>\n",
"\t<li>24</li>\n",
"</ol>\n"
],
"text/latex": [
"\\begin{enumerate*}\n",
"\\item 8519\n",
"\\item 24\n",
"\\end{enumerate*}\n"
],
"text/markdown": [
"1. 8519\n",
"2. 24\n",
"\n",
"\n"
],
"text/plain": [
"[1] 8519 24"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"rma_doce_BrainArray <- affy::justRMA(celfile.path=cel_file_dir,sampleNames=snames,\n",
" verbose=FALSE,compress=FALSE,cdfname=customAnno$customCDFname)\n",
"annotation(rma_doce_BrainArray)\n",
"dim(exprs(rma_doce_BrainArray))"
]
},
{
"cell_type": "code",
"execution_count": 94,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th></th><th scope=col>GSM4901</th><th scope=col>GSM4902</th><th scope=col>GSM4903</th><th scope=col>GSM4904</th><th scope=col>GSM4905</th><th scope=col>GSM4906</th><th scope=col>GSM4907</th><th scope=col>GSM4908</th><th scope=col>GSM4909</th><th scope=col>GSM4910</th><th scope=col>⋯</th><th scope=col>GSM4915</th><th scope=col>GSM4916</th><th scope=col>GSM4917</th><th scope=col>GSM4918</th><th scope=col>GSM4919</th><th scope=col>GSM4920</th><th scope=col>GSM4921</th><th scope=col>GSM4922</th><th scope=col>GSM4923</th><th scope=col>GSM4924</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><th scope=row>AADAC</th><td>4,246572 </td><td>3,988715 </td><td>3,387175 </td><td>3,692939 </td><td>4,710232 </td><td> 3,788563</td><td> 3,564630</td><td>4,843054 </td><td>4,567442 </td><td>4,268574 </td><td>⋯ </td><td>3,992699 </td><td>3,724247 </td><td>3,401156 </td><td>4,314926 </td><td>5,820770 </td><td>3,928832 </td><td>3,613545 </td><td>4,031425 </td><td>4,874323 </td><td>4,207930 </td></tr>\n",
"\t<tr><th scope=row>AAK1</th><td>3,503150 </td><td>3,481343 </td><td>3,267147 </td><td>3,799788 </td><td>3,946391 </td><td> 3,486923</td><td> 3,310952</td><td>3,370090 </td><td>4,033090 </td><td>3,521773 </td><td>⋯ </td><td>3,365616 </td><td>3,448040 </td><td>3,277319 </td><td>3,483527 </td><td>3,256345 </td><td>3,302839 </td><td>3,270803 </td><td>3,507228 </td><td>3,485034 </td><td>3,427167 </td></tr>\n",
"\t<tr><th scope=row>AAMP</th><td>6,542812 </td><td>6,433155 </td><td>7,112246 </td><td>6,726937 </td><td>7,048852 </td><td> 6,697682</td><td> 7,044337</td><td>6,983283 </td><td>6,968767 </td><td>6,134034 </td><td>⋯ </td><td>7,542823 </td><td>6,242356 </td><td>7,463244 </td><td>7,561346 </td><td>6,944381 </td><td>7,543045 </td><td>7,032896 </td><td>6,401135 </td><td>6,753362 </td><td>6,682369 </td></tr>\n",
"\t<tr><th scope=row>AANAT</th><td>8,262640 </td><td>7,809070 </td><td>7,429048 </td><td>7,881925 </td><td>8,636162 </td><td> 7,612333</td><td> 7,747587</td><td>7,630458 </td><td>8,497340 </td><td>7,720368 </td><td>⋯ </td><td>7,899382 </td><td>7,625594 </td><td>7,761377 </td><td>7,922388 </td><td>7,437147 </td><td>7,905339 </td><td>7,712204 </td><td>7,772773 </td><td>7,795030 </td><td>7,620933 </td></tr>\n",
"\t<tr><th scope=row>AARS</th><td>8,715532 </td><td>9,549540 </td><td>8,925394 </td><td>9,426015 </td><td>8,139263 </td><td>10,383877</td><td>10,094132</td><td>8,438800 </td><td>8,857150 </td><td>8,694890 </td><td>⋯ </td><td>9,162233 </td><td>9,401812 </td><td>9,758292 </td><td>8,780993 </td><td>9,141654 </td><td>9,511462 </td><td>9,582736 </td><td>8,506947 </td><td>8,874166 </td><td>8,419377 </td></tr>\n",
"\t<tr><th scope=row>AASDHPPT</th><td>7,313638 </td><td>7,208273 </td><td>8,728579 </td><td>7,394029 </td><td>6,499497 </td><td> 7,896952</td><td> 8,509394</td><td>7,753057 </td><td>6,754180 </td><td>9,084544 </td><td>⋯ </td><td>7,292513 </td><td>8,133136 </td><td>7,531076 </td><td>7,058344 </td><td>7,443340 </td><td>7,703600 </td><td>7,198549 </td><td>8,290108 </td><td>8,486498 </td><td>7,723431 </td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|llllllllllllllllllllllll}\n",
" & GSM4901 & GSM4902 & GSM4903 & GSM4904 & GSM4905 & GSM4906 & GSM4907 & GSM4908 & GSM4909 & GSM4910 & ⋯ & GSM4915 & GSM4916 & GSM4917 & GSM4918 & GSM4919 & GSM4920 & GSM4921 & GSM4922 & GSM4923 & GSM4924\\\\\n",
"\\hline\n",
"\tAADAC & 4,246572 & 3,988715 & 3,387175 & 3,692939 & 4,710232 & 3,788563 & 3,564630 & 4,843054 & 4,567442 & 4,268574 & ⋯ & 3,992699 & 3,724247 & 3,401156 & 4,314926 & 5,820770 & 3,928832 & 3,613545 & 4,031425 & 4,874323 & 4,207930 \\\\\n",
"\tAAK1 & 3,503150 & 3,481343 & 3,267147 & 3,799788 & 3,946391 & 3,486923 & 3,310952 & 3,370090 & 4,033090 & 3,521773 & ⋯ & 3,365616 & 3,448040 & 3,277319 & 3,483527 & 3,256345 & 3,302839 & 3,270803 & 3,507228 & 3,485034 & 3,427167 \\\\\n",
"\tAAMP & 6,542812 & 6,433155 & 7,112246 & 6,726937 & 7,048852 & 6,697682 & 7,044337 & 6,983283 & 6,968767 & 6,134034 & ⋯ & 7,542823 & 6,242356 & 7,463244 & 7,561346 & 6,944381 & 7,543045 & 7,032896 & 6,401135 & 6,753362 & 6,682369 \\\\\n",
"\tAANAT & 8,262640 & 7,809070 & 7,429048 & 7,881925 & 8,636162 & 7,612333 & 7,747587 & 7,630458 & 8,497340 & 7,720368 & ⋯ & 7,899382 & 7,625594 & 7,761377 & 7,922388 & 7,437147 & 7,905339 & 7,712204 & 7,772773 & 7,795030 & 7,620933 \\\\\n",
"\tAARS & 8,715532 & 9,549540 & 8,925394 & 9,426015 & 8,139263 & 10,383877 & 10,094132 & 8,438800 & 8,857150 & 8,694890 & ⋯ & 9,162233 & 9,401812 & 9,758292 & 8,780993 & 9,141654 & 9,511462 & 9,582736 & 8,506947 & 8,874166 & 8,419377 \\\\\n",
"\tAASDHPPT & 7,313638 & 7,208273 & 8,728579 & 7,394029 & 6,499497 & 7,896952 & 8,509394 & 7,753057 & 6,754180 & 9,084544 & ⋯ & 7,292513 & 8,133136 & 7,531076 & 7,058344 & 7,443340 & 7,703600 & 7,198549 & 8,290108 & 8,486498 & 7,723431 \\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"| <!--/--> | GSM4901 | GSM4902 | GSM4903 | GSM4904 | GSM4905 | GSM4906 | GSM4907 | GSM4908 | GSM4909 | GSM4910 | ⋯ | GSM4915 | GSM4916 | GSM4917 | GSM4918 | GSM4919 | GSM4920 | GSM4921 | GSM4922 | GSM4923 | GSM4924 | \n",
"|---|---|---|---|---|---|\n",
"| AADAC | 4,246572 | 3,988715 | 3,387175 | 3,692939 | 4,710232 | 3,788563 | 3,564630 | 4,843054 | 4,567442 | 4,268574 | ⋯ | 3,992699 | 3,724247 | 3,401156 | 4,314926 | 5,820770 | 3,928832 | 3,613545 | 4,031425 | 4,874323 | 4,207930 | \n",
"| AAK1 | 3,503150 | 3,481343 | 3,267147 | 3,799788 | 3,946391 | 3,486923 | 3,310952 | 3,370090 | 4,033090 | 3,521773 | ⋯ | 3,365616 | 3,448040 | 3,277319 | 3,483527 | 3,256345 | 3,302839 | 3,270803 | 3,507228 | 3,485034 | 3,427167 | \n",
"| AAMP | 6,542812 | 6,433155 | 7,112246 | 6,726937 | 7,048852 | 6,697682 | 7,044337 | 6,983283 | 6,968767 | 6,134034 | ⋯ | 7,542823 | 6,242356 | 7,463244 | 7,561346 | 6,944381 | 7,543045 | 7,032896 | 6,401135 | 6,753362 | 6,682369 | \n",
"| AANAT | 8,262640 | 7,809070 | 7,429048 | 7,881925 | 8,636162 | 7,612333 | 7,747587 | 7,630458 | 8,497340 | 7,720368 | ⋯ | 7,899382 | 7,625594 | 7,761377 | 7,922388 | 7,437147 | 7,905339 | 7,712204 | 7,772773 | 7,795030 | 7,620933 | \n",
"| AARS | 8,715532 | 9,549540 | 8,925394 | 9,426015 | 8,139263 | 10,383877 | 10,094132 | 8,438800 | 8,857150 | 8,694890 | ⋯ | 9,162233 | 9,401812 | 9,758292 | 8,780993 | 9,141654 | 9,511462 | 9,582736 | 8,506947 | 8,874166 | 8,419377 | \n",
"| AASDHPPT | 7,313638 | 7,208273 | 8,728579 | 7,394029 | 6,499497 | 7,896952 | 8,509394 | 7,753057 | 6,754180 | 9,084544 | ⋯ | 7,292513 | 8,133136 | 7,531076 | 7,058344 | 7,443340 | 7,703600 | 7,198549 | 8,290108 | 8,486498 | 7,723431 | \n",
"\n",
"\n"
],
"text/plain": [
" GSM4901 GSM4902 GSM4903 GSM4904 GSM4905 GSM4906 GSM4907 \n",
"AADAC 4,246572 3,988715 3,387175 3,692939 4,710232 3,788563 3,564630\n",
"AAK1 3,503150 3,481343 3,267147 3,799788 3,946391 3,486923 3,310952\n",
"AAMP 6,542812 6,433155 7,112246 6,726937 7,048852 6,697682 7,044337\n",
"AANAT 8,262640 7,809070 7,429048 7,881925 8,636162 7,612333 7,747587\n",
"AARS 8,715532 9,549540 8,925394 9,426015 8,139263 10,383877 10,094132\n",
"AASDHPPT 7,313638 7,208273 8,728579 7,394029 6,499497 7,896952 8,509394\n",
" GSM4908 GSM4909 GSM4910 ⋯ GSM4915 GSM4916 GSM4917 GSM4918 \n",
"AADAC 4,843054 4,567442 4,268574 ⋯ 3,992699 3,724247 3,401156 4,314926\n",
"AAK1 3,370090 4,033090 3,521773 ⋯ 3,365616 3,448040 3,277319 3,483527\n",
"AAMP 6,983283 6,968767 6,134034 ⋯ 7,542823 6,242356 7,463244 7,561346\n",
"AANAT 7,630458 8,497340 7,720368 ⋯ 7,899382 7,625594 7,761377 7,922388\n",
"AARS 8,438800 8,857150 8,694890 ⋯ 9,162233 9,401812 9,758292 8,780993\n",
"AASDHPPT 7,753057 6,754180 9,084544 ⋯ 7,292513 8,133136 7,531076 7,058344\n",
" GSM4919 GSM4920 GSM4921 GSM4922 GSM4923 GSM4924 \n",
"AADAC 5,820770 3,928832 3,613545 4,031425 4,874323 4,207930\n",
"AAK1 3,256345 3,302839 3,270803 3,507228 3,485034 3,427167\n",
"AAMP 6,944381 7,543045 7,032896 6,401135 6,753362 6,682369\n",
"AANAT 7,437147 7,905339 7,712204 7,772773 7,795030 7,620933\n",
"AARS 9,141654 9,511462 9,582736 8,506947 8,874166 8,419377\n",
"AASDHPPT 7,443340 7,703600 7,198549 8,290108 8,486498 7,723431"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"<ol class=list-inline>\n",
"\t<li>8449</li>\n",
"\t<li>24</li>\n",
"</ol>\n"
],
"text/latex": [
"\\begin{enumerate*}\n",
"\\item 8449\n",
"\\item 24\n",
"\\end{enumerate*}\n"
],
"text/markdown": [
"1. 8449\n",
"2. 24\n",
"\n",
"\n"
],
"text/plain": [
"[1] 8449 24"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"anno_SYMBOL <- suppressMessages(select(get(customAnno$customDBname), keytype=\"PROBEID\", \n",
" columns=c(\"SYMBOL\"), keys=row.names(exprs(rma_doce_BrainArray))))\n",
"anno_SYMBOL <- anno_SYMBOL[!is.na(anno_SYMBOL$SYMBOL),]\n",
"CR <- WGCNA::collapseRows(exprs(rma_doce_BrainArray), rowGroup = anno_SYMBOL$SYMBOL, rowID = anno_SYMBOL$PROBEID\n",
" ,method=\"Average\")\n",
"exprs_rma_doce_BrainArray<- CR$datETcollapsed\n",
"write.table(exprs_rma_doce_BrainArray, file =\"Geeleher_with_GDSCr6/data/GSE6434.BrainArray.RMAlog2Average.Symbol.Expr.tsv\",na=\"\",quote = FALSE,sep=\"\\t\")\n",
"head(exprs_rma_doce_BrainArray)\n",
"dim(exprs_rma_doce_BrainArray)"
]
},
{
"cell_type": "code",
"execution_count": 95,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th></th><th scope=col>GSM4901</th><th scope=col>GSM4902</th><th scope=col>GSM4903</th><th scope=col>GSM4904</th><th scope=col>GSM4905</th><th scope=col>GSM4906</th><th scope=col>GSM4907</th><th scope=col>GSM4908</th><th scope=col>GSM4909</th><th scope=col>GSM4910</th><th scope=col>⋯</th><th scope=col>GSM4915</th><th scope=col>GSM4916</th><th scope=col>GSM4917</th><th scope=col>GSM4918</th><th scope=col>GSM4919</th><th scope=col>GSM4920</th><th scope=col>GSM4921</th><th scope=col>GSM4922</th><th scope=col>GSM4923</th><th scope=col>GSM4924</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><th scope=row>10</th><td>3,352156</td><td>3,308508</td><td>3,096914</td><td>3,236103</td><td>3,811192</td><td>3,104723</td><td>3,081062</td><td>3,091837</td><td>3,949944</td><td>3,622625</td><td>⋯ </td><td>3,136446</td><td>3,491678</td><td>3,365999</td><td>3,622488</td><td>3,450723</td><td>3,396406</td><td>3,453915</td><td>3,612785</td><td>3,148515</td><td>3,275832</td></tr>\n",
"\t<tr><th scope=row>100</th><td>6,737301</td><td>6,659171</td><td>6,455985</td><td>6,695844</td><td>6,965612</td><td>6,603501</td><td>6,461829</td><td>6,246567</td><td>7,155956</td><td>6,826456</td><td>⋯ </td><td>6,775504</td><td>6,891247</td><td>6,983027</td><td>6,862854</td><td>6,768173</td><td>6,709703</td><td>6,484590</td><td>6,502096</td><td>6,745475</td><td>6,842699</td></tr>\n",
"\t<tr><th scope=row>1000</th><td>3,834283</td><td>3,677712</td><td>3,396575</td><td>3,723289</td><td>3,450899</td><td>3,545390</td><td>3,474213</td><td>3,298312</td><td>3,681804</td><td>3,471742</td><td>⋯ </td><td>3,329445</td><td>3,611272</td><td>3,160738</td><td>3,487775</td><td>3,264067</td><td>3,476193</td><td>3,115201</td><td>3,433925</td><td>3,154068</td><td>3,239380</td></tr>\n",
"\t<tr><th scope=row>10000</th><td>4,754271</td><td>4,496707</td><td>4,483903</td><td>4,585342</td><td>5,254096</td><td>4,824657</td><td>4,610763</td><td>4,705913</td><td>4,544194</td><td>4,187782</td><td>⋯ </td><td>5,769203</td><td>4,751104</td><td>4,562195</td><td>4,366119</td><td>5,410028</td><td>4,297884</td><td>4,593181</td><td>4,197862</td><td>4,547317</td><td>4,246281</td></tr>\n",
"\t<tr><th scope=row>10001</th><td>3,424575</td><td>3,490181</td><td>3,820446</td><td>3,465579</td><td>3,489038</td><td>3,349595</td><td>3,558470</td><td>3,299228</td><td>3,656393</td><td>3,511745</td><td>⋯ </td><td>3,746529</td><td>3,405819</td><td>3,760430</td><td>3,949115</td><td>3,669616</td><td>3,876380</td><td>3,835922</td><td>4,054287</td><td>3,528116</td><td>3,664227</td></tr>\n",
"\t<tr><th scope=row>10002</th><td>7,934315</td><td>7,757096</td><td>7,293050</td><td>7,820109</td><td>8,616442</td><td>7,514208</td><td>7,403382</td><td>7,470628</td><td>8,706345</td><td>8,217301</td><td>⋯ </td><td>7,802912</td><td>8,219931</td><td>8,165052</td><td>8,235681</td><td>7,045313</td><td>7,998694</td><td>7,701926</td><td>7,857424</td><td>7,532069</td><td>8,243082</td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|llllllllllllllllllllllll}\n",
" & GSM4901 & GSM4902 & GSM4903 & GSM4904 & GSM4905 & GSM4906 & GSM4907 & GSM4908 & GSM4909 & GSM4910 & ⋯ & GSM4915 & GSM4916 & GSM4917 & GSM4918 & GSM4919 & GSM4920 & GSM4921 & GSM4922 & GSM4923 & GSM4924\\\\\n",
"\\hline\n",
"\t10 & 3,352156 & 3,308508 & 3,096914 & 3,236103 & 3,811192 & 3,104723 & 3,081062 & 3,091837 & 3,949944 & 3,622625 & ⋯ & 3,136446 & 3,491678 & 3,365999 & 3,622488 & 3,450723 & 3,396406 & 3,453915 & 3,612785 & 3,148515 & 3,275832\\\\\n",
"\t100 & 6,737301 & 6,659171 & 6,455985 & 6,695844 & 6,965612 & 6,603501 & 6,461829 & 6,246567 & 7,155956 & 6,826456 & ⋯ & 6,775504 & 6,891247 & 6,983027 & 6,862854 & 6,768173 & 6,709703 & 6,484590 & 6,502096 & 6,745475 & 6,842699\\\\\n",
"\t1000 & 3,834283 & 3,677712 & 3,396575 & 3,723289 & 3,450899 & 3,545390 & 3,474213 & 3,298312 & 3,681804 & 3,471742 & ⋯ & 3,329445 & 3,611272 & 3,160738 & 3,487775 & 3,264067 & 3,476193 & 3,115201 & 3,433925 & 3,154068 & 3,239380\\\\\n",
"\t10000 & 4,754271 & 4,496707 & 4,483903 & 4,585342 & 5,254096 & 4,824657 & 4,610763 & 4,705913 & 4,544194 & 4,187782 & ⋯ & 5,769203 & 4,751104 & 4,562195 & 4,366119 & 5,410028 & 4,297884 & 4,593181 & 4,197862 & 4,547317 & 4,246281\\\\\n",
"\t10001 & 3,424575 & 3,490181 & 3,820446 & 3,465579 & 3,489038 & 3,349595 & 3,558470 & 3,299228 & 3,656393 & 3,511745 & ⋯ & 3,746529 & 3,405819 & 3,760430 & 3,949115 & 3,669616 & 3,876380 & 3,835922 & 4,054287 & 3,528116 & 3,664227\\\\\n",
"\t10002 & 7,934315 & 7,757096 & 7,293050 & 7,820109 & 8,616442 & 7,514208 & 7,403382 & 7,470628 & 8,706345 & 8,217301 & ⋯ & 7,802912 & 8,219931 & 8,165052 & 8,235681 & 7,045313 & 7,998694 & 7,701926 & 7,857424 & 7,532069 & 8,243082\\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"| <!--/--> | GSM4901 | GSM4902 | GSM4903 | GSM4904 | GSM4905 | GSM4906 | GSM4907 | GSM4908 | GSM4909 | GSM4910 | ⋯ | GSM4915 | GSM4916 | GSM4917 | GSM4918 | GSM4919 | GSM4920 | GSM4921 | GSM4922 | GSM4923 | GSM4924 | \n",
"|---|---|---|---|---|---|\n",
"| 10 | 3,352156 | 3,308508 | 3,096914 | 3,236103 | 3,811192 | 3,104723 | 3,081062 | 3,091837 | 3,949944 | 3,622625 | ⋯ | 3,136446 | 3,491678 | 3,365999 | 3,622488 | 3,450723 | 3,396406 | 3,453915 | 3,612785 | 3,148515 | 3,275832 | \n",
"| 100 | 6,737301 | 6,659171 | 6,455985 | 6,695844 | 6,965612 | 6,603501 | 6,461829 | 6,246567 | 7,155956 | 6,826456 | ⋯ | 6,775504 | 6,891247 | 6,983027 | 6,862854 | 6,768173 | 6,709703 | 6,484590 | 6,502096 | 6,745475 | 6,842699 | \n",
"| 1000 | 3,834283 | 3,677712 | 3,396575 | 3,723289 | 3,450899 | 3,545390 | 3,474213 | 3,298312 | 3,681804 | 3,471742 | ⋯ | 3,329445 | 3,611272 | 3,160738 | 3,487775 | 3,264067 | 3,476193 | 3,115201 | 3,433925 | 3,154068 | 3,239380 | \n",
"| 10000 | 4,754271 | 4,496707 | 4,483903 | 4,585342 | 5,254096 | 4,824657 | 4,610763 | 4,705913 | 4,544194 | 4,187782 | ⋯ | 5,769203 | 4,751104 | 4,562195 | 4,366119 | 5,410028 | 4,297884 | 4,593181 | 4,197862 | 4,547317 | 4,246281 | \n",
"| 10001 | 3,424575 | 3,490181 | 3,820446 | 3,465579 | 3,489038 | 3,349595 | 3,558470 | 3,299228 | 3,656393 | 3,511745 | ⋯ | 3,746529 | 3,405819 | 3,760430 | 3,949115 | 3,669616 | 3,876380 | 3,835922 | 4,054287 | 3,528116 | 3,664227 | \n",
"| 10002 | 7,934315 | 7,757096 | 7,293050 | 7,820109 | 8,616442 | 7,514208 | 7,403382 | 7,470628 | 8,706345 | 8,217301 | ⋯ | 7,802912 | 8,219931 | 8,165052 | 8,235681 | 7,045313 | 7,998694 | 7,701926 | 7,857424 | 7,532069 | 8,243082 | \n",
"\n",
"\n"
],
"text/plain": [
" GSM4901 GSM4902 GSM4903 GSM4904 GSM4905 GSM4906 GSM4907 GSM4908 \n",
"10 3,352156 3,308508 3,096914 3,236103 3,811192 3,104723 3,081062 3,091837\n",
"100 6,737301 6,659171 6,455985 6,695844 6,965612 6,603501 6,461829 6,246567\n",
"1000 3,834283 3,677712 3,396575 3,723289 3,450899 3,545390 3,474213 3,298312\n",
"10000 4,754271 4,496707 4,483903 4,585342 5,254096 4,824657 4,610763 4,705913\n",
"10001 3,424575 3,490181 3,820446 3,465579 3,489038 3,349595 3,558470 3,299228\n",
"10002 7,934315 7,757096 7,293050 7,820109 8,616442 7,514208 7,403382 7,470628\n",
" GSM4909 GSM4910 ⋯ GSM4915 GSM4916 GSM4917 GSM4918 GSM4919 GSM4920 \n",
"10 3,949944 3,622625 ⋯ 3,136446 3,491678 3,365999 3,622488 3,450723 3,396406\n",
"100 7,155956 6,826456 ⋯ 6,775504 6,891247 6,983027 6,862854 6,768173 6,709703\n",
"1000 3,681804 3,471742 ⋯ 3,329445 3,611272 3,160738 3,487775 3,264067 3,476193\n",
"10000 4,544194 4,187782 ⋯ 5,769203 4,751104 4,562195 4,366119 5,410028 4,297884\n",
"10001 3,656393 3,511745 ⋯ 3,746529 3,405819 3,760430 3,949115 3,669616 3,876380\n",
"10002 8,706345 8,217301 ⋯ 7,802912 8,219931 8,165052 8,235681 7,045313 7,998694\n",
" GSM4921 GSM4922 GSM4923 GSM4924 \n",
"10 3,453915 3,612785 3,148515 3,275832\n",
"100 6,484590 6,502096 6,745475 6,842699\n",
"1000 3,115201 3,433925 3,154068 3,239380\n",
"10000 4,593181 4,197862 4,547317 4,246281\n",
"10001 3,835922 4,054287 3,528116 3,664227\n",
"10002 7,701926 7,857424 7,532069 8,243082"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"anno_ENTREZ <- suppressMessages(select(get(customAnno$customDBname), keytype=\"PROBEID\", \n",
" columns=c(\"ENTREZID\"), keys=row.names(exprs(rma_doce_BrainArray))))\n",
"anno_ENTREZ <- anno_ENTREZ[!is.na(anno_ENTREZ$ENTREZ),]\n",
"CR <- WGCNA::collapseRows(exprs(rma_doce_BrainArray), rowGroup = anno_ENTREZ$ENTREZID,\n",
" rowID = anno_ENTREZ$PROBEID,method=\"Average\")\n",
"exprs_rma_doce_BrainArray_ENTREZ<- CR$datETcollapsed\n",
"write.table(exprs_rma_doce_BrainArray_ENTREZ, file =\"Geeleher_with_GDSCr6/data/GSE6434.BrainArray.RMAlog2Average.Entrez.Expr.tsv\",\n",
" na=\"\",quote = FALSE,sep=\"\\t\")\n",
"head(exprs_rma_doce_BrainArray_ENTREZ)"
]
},
{
"cell_type": "code",
"execution_count": 101,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"8061"
],
"text/latex": [
"8061"
],
"text/markdown": [
"8061"
],
"text/plain": [
"[1] 8061"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"24"
],
"text/latex": [
"24"
],
"text/markdown": [
"24"
],
"text/plain": [
"[1] 24"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"shared_genes <- intersect(row.names((exprs_rma_doce_BrainArray)),row.names(doceVivoNorm_syms))\n",
"length(shared_genes)\n",
"shared_samples <- intersect(colnames((exprs_rma_doce_BrainArray)),colnames(doceVivoNorm_syms))\n",
"length(shared_samples)"
]
},
{
"cell_type": "code",
"execution_count": 102,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<span style=white-space:pre-wrap>'Corr. between genes (mean, max, min) 0,994214009288569 0,999999751668813 -0,0322620349274823'</span>"
],
"text/latex": [
"'Corr. between genes (mean, max, min) 0,994214009288569 0,999999751668813 -0,0322620349274823'"
],
"text/markdown": [
"<span style=white-space:pre-wrap>'Corr. between genes (mean, max, min) 0,994214009288569 0,999999751668813 -0,0322620349274823'</span>"
],
"text/plain": [
"[1] \"Corr. between genes (mean, max, min) 0,994214009288569 0,999999751668813 -0,0322620349274823\""
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"<span style=white-space:pre-wrap>'Corr. between samples (mean, max, min) 0,995224019854658 0,996122633468715 0,993188134393841'</span>"
],
"text/latex": [
"'Corr. between samples (mean, max, min) 0,995224019854658 0,996122633468715 0,993188134393841'"
],
"text/markdown": [
"<span style=white-space:pre-wrap>'Corr. between samples (mean, max, min) 0,995224019854658 0,996122633468715 0,993188134393841'</span>"
],
"text/plain": [
"[1] \"Corr. between samples (mean, max, min) 0,995224019854658 0,996122633468715 0,993188134393841\""
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"gene_corrs <- diag(cor(t(exprs_rma_doce_BrainArray[shared_genes,shared_samples]), t(doceVivoNorm_syms[shared_genes,shared_samples])))\n",
"sample_corrs <- diag(cor(exprs_rma_doce_BrainArray[shared_genes,shared_samples], doceVivoNorm_syms[shared_genes,shared_samples]))\n",
"# average correlation between genes\n",
"paste(\"Corr. between genes (mean, max, min)\",mean(gene_corrs),max(gene_corrs),min(gene_corrs), sep =\" \")\n",
"# average correlation between samples\n",
"paste(\"Corr. between samples (mean, max, min)\",mean(sample_corrs),max(sample_corrs),min(sample_corrs), sep =\" \")"
]
},
{
"cell_type": "code",
"execution_count": 103,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"116"
],
"text/latex": [
"116"
],
"text/markdown": [
"116"
],
"text/plain": [
"[1] 116"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"length(gene_corrs[gene_corrs<0.9])"
]
},
{
"cell_type": "code",
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"R version 3.5.0 (2018-04-23)\n",
"Platform: x86_64-conda_cos6-linux-gnu (64-bit)\n",
"Running under: Ubuntu 16.04.5 LTS\n",
"\n",
"Matrix products: default\n",
"BLAS/LAPACK: /home/olya/miniconda2/lib/R/lib/libRblas.so\n",
"\n",
"locale:\n",
" [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=de_DE.UTF-8 \n",
" [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8 \n",
" [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8 \n",
" [7] LC_PAPER=de_DE.UTF-8 LC_NAME=de_DE.UTF-8 \n",
" [9] LC_ADDRESS=de_DE.UTF-8 LC_TELEPHONE=de_DE.UTF-8 \n",
"[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=de_DE.UTF-8\n",
"\n",
"attached base packages:\n",
"[1] stats4 parallel stats graphics grDevices utils datasets \n",
"[8] methods base \n",
"\n",
"other attached packages:\n",
" [1] hugene10sthsentrezg.db_22.0.0 hugene10sthsentrezgcdf_22.0.0 \n",
" [3] hgu133bhsentrezg.db_22.0.0 hgu133bhsentrezgcdf_22.0.0 \n",
" [5] hgu133ahsentrezg.db_22.0.0 hgu133ahsentrezgcdf_22.0.0 \n",
" [7] hgu95av2hsentrezg.db_22.0.0 hgu95av2hsentrezgcdf_22.0.0 \n",
" [9] hgu133plus2hsentrezg.db_22.0.0 hgu133plus2hsentrezgcdf_22.0.0\n",
"[11] hgu219hsentrezg.db_22.0.0 org.Hs.eg.db_3.4.1 \n",
"[13] hgu219hsentrezgcdf_22.0.0 AnnotationDbi_1.38.2 \n",
"[15] IRanges_2.10.5 S4Vectors_0.14.7 \n",
"[17] affyio_1.46.0 affy_1.54.0 \n",
"[19] Biobase_2.36.2 BiocGenerics_0.22.1 \n",
"\n",
"loaded via a namespace (and not attached):\n",
" [1] matrixStats_0.54.0 fit.models_0.5-14 robust_0.4-18 \n",
" [4] bit64_0.9-7 doParallel_1.0.11 RColorBrewer_1.1-2 \n",
" [7] repr_0.15.0 dynamicTreeCut_1.63-1 tools_3.5.0 \n",
"[10] backports_1.1.2 R6_2.2.2 rpart_4.1-13 \n",
"[13] Hmisc_4.1-1 DBI_1.0.0 lazyeval_0.2.1 \n",
"[16] colorspace_1.3-2 nnet_7.3-12 tidyselect_0.2.4 \n",
"[19] gridExtra_2.3 bit_1.1-14 compiler_3.5.0 \n",
"[22] preprocessCore_1.38.1 WGCNA_1.64-1 htmlTable_1.12 \n",
"[25] scales_1.0.0 checkmate_1.8.5 mvtnorm_1.0-8 \n",
"[28] DEoptimR_1.0-8 robustbase_0.93-2 pbdZMQ_0.3-3 \n",
"[31] stringr_1.3.1 digest_0.6.17 foreign_0.8-71 \n",
"[34] rrcov_1.4-4 base64enc_0.1-3 pkgconfig_2.0.2 \n",
"[37] htmltools_0.3.6 htmlwidgets_1.2 rlang_0.2.2 \n",
"[40] impute_1.50.1 rstudioapi_0.7 RSQLite_2.1.1 \n",
"[43] BiocInstaller_1.26.1 bindr_0.1.1 jsonlite_1.5 \n",
"[46] acepack_1.4.1 dplyr_0.7.6 magrittr_1.5 \n",
"[49] GO.db_3.4.1 Formula_1.2-3 Matrix_1.2-14 \n",
"[52] Rcpp_0.12.18 IRkernel_0.8.11 munsell_0.5.0 \n",
"[55] stringi_1.2.4 MASS_7.3-50 zlibbioc_1.22.0 \n",
"[58] plyr_1.8.4 grid_3.5.0 blob_1.1.1 \n",
"[61] crayon_1.3.4 lattice_0.20-35 IRdisplay_0.5.0 \n",
"[64] splines_3.5.0 knitr_1.20 pillar_1.3.0 \n",
"[67] fastcluster_1.1.25 uuid_0.1-2 codetools_0.2-15 \n",
"[70] glue_1.3.0 evaluate_0.11 latticeExtra_0.6-28 \n",
"[73] data.table_1.11.4 foreach_1.4.4 gtable_0.2.0 \n",
"[76] purrr_0.2.5 assertthat_0.2.0 ggplot2_3.0.0 \n",
"[79] pcaPP_1.9-73 survival_2.42-6 tibble_1.4.2 \n",
"[82] iterators_1.0.10 memoise_1.1.0 bindrcpp_0.2.2 \n",
"[85] cluster_2.0.7-1 "
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Datasets
Models
