CPM or TPM values as discretization method input
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4 weeks ago
antmantras • 0

Dear all, I have a question regarding which input should I use for a downstream analysis pipeline.

I want to select differentially expressed genes in an RNA-Seq dataset (RSEM estimated counts) with paired data in cancer (cancer vs healthy). Then, I need to discretize the expression values of the differentially expressed genes for downstream analysis.

I have been reading various sources and have concluded that I need the expression values as TPMs or CPMs. I know that I need to correct for library size but I don't think that gene length bias would impact the discretization process. So right now CPM or log2(CPM + 2) output from edgeR should be more suitable for my intended. Am I right about this? Thanks in advance.

RNA-Seq discretization TPM CPM • 97 views
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