Question

FPKM for TMM

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2.8 years ago

bioinfo ▴ 60

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

TMM normalization • 916 views

ADD COMMENT • link updated 2.8 years ago by ATpoint 81k • written 2.8 years ago by bioinfo ▴ 60

score 1 · Answer 1 · 2021-06-30

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2.8 years ago

i.sudbery 19k

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

ADD COMMENT • link 2.8 years ago by i.sudbery 19k

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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?

ADD REPLY • link 2.8 years ago by ATpoint 81k