Question

Robustness of Different Normalization Approaches

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3.8 years ago

Jay-Run ▴ 30

Why exactly TMM normalization (implemented in edgeR) is more robust than RLE normalization (implemented in DESeq2)?

RNA-Seq DESeq2 edgeR • 1.4k views

ADD COMMENT • link updated 3.8 years ago by Biostar 20 • written 3.8 years ago by Jay-Run ▴ 30

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ADD REPLY • link 3.8 years ago by ATpoint 85k

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Care to elaborate please? Is this a "citation request" to edgeR and DESeq? :)

ADD REPLY • link 3.8 years ago by Jay-Run ▴ 30

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Who said it was?

Most real world explorations of normalization methods find that RLE and TMM perform more or less the same.

ADD REPLY • link 3.8 years ago by i.sudbery 20k

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Thanks! Maybe I should have asked: "Is TMM more robust than RLE?" If yes, in what situations?

ADD REPLY • link 3.8 years ago by Jay-Run ▴ 30

score 3 · Answer 1 · 2021-01-30

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3.8 years ago

seidel 11k

Yes, @ATpoint was asking for a reference to support your supposition: "TMM normalization is more robust than RLE". You can read about about the differences in "In Papyro Comparison of TMM (edgeR), RLE (DESeq2), and MRN Normalization Methods" and "Why are normalization methods not interchangeable?". Both contain descriptions of situations that might favor one or the other.