TPM data Differential expression analysis
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ghmdsr • 0
@ghmdsr-15634
Last seen 3.9 years ago

I'm  graduate-student in bioinformatics.

i want test my algorithm with TCGA expression data.

This data has TPM value. (so i can't get read count for EdgeR)

I've done DEG analysis to read count with EdgeR.

But this time, I got TPM value which would be used in EdgeR.

How can i analyze differential expression with TPM data? 

edger limma differential gene expression • 5.4k views
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@gordon-smyth
Last seen 9 minutes ago
WEHI, Melbourne, Australia

Despite their popularity, TPM values are really only for description purposes and are not suitable for DE analyses. There is no entirely satisfactory way to do a DE analysis of TPM values. See comments I made previously about FPKM:

A: Differential expression of RNA-seq data using limma and voom()

Everything I said about FPKM applies equally well to TPM.

What many people do is a limma-trend analysis of log2(TPM+1). I've never done that myself, but I can't think of anything better if all you have are TPM.

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Hi Gordon Smyth,

Question on your above answer: I have logTPM normalized data. Can I perform DE analysis using it on EdgeR, instead of inputting raw data? Thank you!

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I have nothing to add my previous answers, which seem to cover everything.

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