TPM RNA-seq data for differential expression analysis

Question

[Catalin-George]

Hello

I have a project where I need to identify differences in gene expression between two categories of cancer patients: low and high survival rate. I am retrieving RNA seq data from the Cancer Genome Atlas TCGA, but I can only find it in the TPM normalized format, or z-scores.

I understand that most R packages used for differential expression analysis (DESeq2, limma/voom, EdgeR) require raw counts, but I am not able to find that. Do you have any suggestions on what I could do with the TPM or z-scores values in order to get some results on which genes are differentially expressed between long and short survival rates.

Thank you!

[Zhenyu Zhang]

GDC has count, tpm, fpkm, uqfpkm in the same count file for all TCGA projects.

Answer 1

[ATpoint]

recount has TCGA raw data: https://bioconductor.org/packages/devel/workflows/vignettes/recountWorkflow/inst/doc/recount-workflow.html