{"cohort":"MET500 (expression centric)","probeMap":"probeMap/gencode.v23.annotation.gene.probemap","dataSubType":"gene expression","citation":"Nature. 2017 Aug 17;548(7667):297-303. doi: 10.1038/nature23306.","label":"RNAseq log2(fpkm)","articletitle":"Integrative clinical genomics of metastatic cancer.","name":"MET500/geneExpression/M.mx.log2.txt","dataproducer":"Robinson DR, Wu YM, ... , Cie\u015blik M, Chinnaiyan AM","wrangling_procedure":"download fpkm data matrix provided by manuscript author, Log2(x+0.001) transform the data matrix","type":"genomicMatrix","version":"2018-12-19","unit":"log2(fpkm+0.001)","colnormalization":true,"pmid":28783718,"description":"The gene expression data is generated using two platforms - capture and polyA RNA-seq. The provided FPKMs matrix has been adjusted for systematic differences between them (capture is changed to look like polyA). The data was obtained by aligning to GRCh38 using STAR and counting reads using featureCounts and the Gencode v.23 reference transcriptome. Only protein coding genes are included because the capture RNA-seq assay is restricted to proteins. For more information please see <a href=\"https://www.nature.com/articles/nature23306#methods\"> method section of the publication</a>. Log2(x+0.001) transformation is applied to convert fpkm values to data in this dataset matrix."}

{"cohort":"MET500 (expression centric)","probeMap":"probeMap/gencode.v23.annotation.gene.probemap","dataSubType":"gene expression","citation":"Nature. 2017 Aug 17;548(7667):297-303. doi: 10.1038/nature23306.","label":"RNAseq zscore","articletitle":"Integrative clinical genomics of metastatic cancer.","name":"MET500/geneExpression/M.mx.log2.zscore.txt","dataproducer":"Robinson DR, Wu YM, ... , Cie\u015blik M, Chinnaiyan AM","wrangling_procedure":"download fpkm data matrix provided by manuscript author, Log2(x+0.001) transform the data matrix, z score tranform each sample independently","type":"genomicMatrix","version":"2018-12-19","unit":"z score","colnormalization":true,"pmid":28783718,"description":"The gene expression data is generated using two platforms - capture and polyA RNA-seq. The provided FPKMs matrix has been adjusted for systematic differences between them (capture is changed to look like polyA). The data was obtained by aligning to GRCh38 using STAR and counting reads using featureCounts and the Gencode v.23 reference transcriptome. Only protein coding genes are included because the capture RNA-seq assay is restricted to proteins. For more information please see <a href=\"https://www.nature.com/articles/nature23306#methods\"> method section of the publication</a>. Log2(x+0.001) transformation, followed by z score transformation (for each sample independently) are applied to convert fpkm values to data in this data matrix."}