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Old 08-19-2014, 09:14 AM   #8
Location: UK

Join Date: Jun 2011
Posts: 61

Originally Posted by Gordon Smyth View Post
Well, the cpm values are fully normalized. The issue is rather that the cpm values produced by cpm() are just for descriptive purposes. They are not used by any of the core functions in edgeR which estimate parameters or evaluate differential expression.
Now I am confused again. And maybe I am not the only one as the response by James MacDonald in the bioconductor thread indicates. I believe this confusion is due to the fact that "normalization" in edgeR seems to mean different things depending on the context. I might be a bit naive but to me any transformation performed on the raw score prior to computing differential expression can be described as "normalisation". This would include library size scaling, TMM, pseudocounts. You seemed to agree with James' response and he literally said "The counts are not affected by the normalization".

Now you seem to say exactly the opposite. Can you, please, clarify?

What I can say with certainty is that no pseudo-counts seem to have been added to the raw counts otherwise I wouldn't have observed the zeros. What is not clear to me whether both library scaling and TMM normalisation have been applied.
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