Statistics on RNAseq data
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5 weeks ago

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

on Statistics data RNAseq • 319 views
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Yes..!! you can do T test.

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

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yeah I can understand that..!

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is not that easy: link

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5 weeks ago

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.

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5 weeks ago
ATpoint 54k

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

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