FPKM for TMM

Question

[bioinfo]

Hi Can FPKM values be normalized again using TMM normalization? Please suggest.

Answer 1

[i.sudbery]

There is no reason you can't use a Trimmed Mean of M-values (TMM) approach for normalizing FPKM values. You might ask if it is the correct approach to take though. I'm also not sure I know of tools that will do it.

You might check out https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2246-7

[ATpoint]

Technically calcNormFactors from edgeR will accept any numeric matrix and then apply its magic to derive normalization factors. I am not sure it expects a certain distribution, probably not, as long as the basic assumption holds that most genes or at least a notable fraction does not change. @OP, what do you plan downstream, something like limma?