Question: Normalized count in edger
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20 days ago by
mzillur0
mzillur0 wrote:

Hello there, How can we find the normalized count from the count data in edger? It seems there are two opposite ways to derive normalized count from the count data. 1. normalized counts=counts*norm.factor 2. normalized counts=counts/norm.factor Which one is right? Best Regards Zillur

edger • 75 views
modified 19 days ago by theodore.georgomanolis0 • written 20 days ago by mzillur0
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20 days ago by
Gordon Smyth37k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth37k wrote:

Neither of your suggestions are correct -- the quantities you suggest don't really have any meaning.

Please see the section on normalization in the edgeR User's Guide. The normalization factors in edgeR serve to normalize the library sizes rather than the counts themselves. In fact, as I have said before on this forum, there is no such thing as a "normalized count" because any quantified expression value that accounts for library size or gene length could no longer be a count. It would help to know what you are trying to achieve, but the cpm or rpkm functions might be what you are looking for.

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19 days ago by
Germany

I recently found those explanatory videos that are quite helpful. in the same series there is a DeSeq2 tutorial

StatQuest: edgeR, part 1, Library Normalization

edit: fixed wrong links and description