Question: TCGA RNA-Seq: are RSEM or Z-scores based expression comparable to each other?
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gravatar for lefthandgergo
19 months ago by
lefthandgergo10 wrote:

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 • 1.2k views
ADD COMMENTlink written 19 months ago by lefthandgergo10

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

ADD REPLYlink written 19 months ago by Matina180

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

ADD REPLYlink written 19 months ago by lefthandgergo10
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