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

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
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updated by ATpoint ATpoint • written by nvera • nvera

1 answer

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

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written by ATpoint ATpoint

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.

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written by nvera • nvera

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

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written by ATpoint ATpoint

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