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TCGA RNA-Seq: are RSEM or Z-scores based expression comparable to each other?

Hi! I'd like to compare expression levels of given genes between two subgroups of the TCGA cohort. I have expression data, derived from the PanCancer Atlas, from cbioportal in two different files: "data_RNA_Seq_v2_expression_median.txt" (RSEM) and "data_RNA_Seq_v2_mRNA_median_Zscores.txt". Which could I use for comparing expression levels between sample groups? Or both of them can be used for this purpose?

Thanks!

rna-seq tcga
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written by lefthandgergo • lefthandgergo

Hi, by "comparing expression levels between sample groups" you mean differential expression analysis?

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written by Matina Matina

Actually what I plan is to collect all expression values for each group, and then look for significant differences between them using Wilcoxon test.

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written by lefthandgergo • lefthandgergo

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