Question

What is the best normalization method for raw RNA-seq counts to be comparable between samples?

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2.9 years ago

nvera ▴ 10

I have used TMM for such purposes but I am not sure that it was the best choice. I want a normalization method that allows me to compare the expression level of any particular gene between two samples (and consequently between any grouping of the samples).

Thanks.

RNA-seq TMM normalization • 944 views

ADD COMMENT • link updated 2.9 years ago by ATpoint 85k • written 2.9 years ago by nvera ▴ 10

score 1 · Answer 1 · 2021-12-21

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2.9 years ago

ATpoint 85k

Yes, it is a fully valid choice. Be sure to use dedicated software for the comparisons, no hand-made statistics.

ADD COMMENT • link 2.9 years ago by ATpoint 85k

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Thanks.

Which software would you recommend?

I just did the TMM normalization with edgeR and started applying statistical tests to compare between groups such as the Mann-Whitney test.

ADD REPLY • link 2.9 years ago by nvera ▴ 10

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Use edgeR, not MWU. edgeR is developed for RNA-seq, MWU is not.

ADD REPLY • link 2.9 years ago by ATpoint 85k