Statistics on RNAseq data

Question

[margot.27.muller]

Hi

I would like to know whether you can do statistical tests (e.g. ANOVAS etc.) on the TPM/RPKM counts of RNAseq data?

Thanks

[hafiz.talhamalik]

Yes..!! you can do T test.

[ATpoint]

You technically can, but this ignores 20 years of biostats research that came up with better strategies.

[hafiz.talhamalik]

yeah I can understand that..!

[andres.firrincieli]

is not that easy: link

Answer 1

[rpolicastro]

This is not recommended due to a few underlying problems with RNA-seq data that include compositional bias, library size differences, and correlation between mean and variance. I won't go into these concepts in detail but use software designed to account for these problems such as DESeq2 or edgeR. Their manuals will have more information on the above concepts.

Answer 2

[ATpoint]

Ah, the never ending question: I usually link this thread here from the limma/edgeR developer which discusses strategies if you only have normalized counts and need to deal with it: https://support.bioconductor.org/p/125144/#125156