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
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
rpkm functions might be what you are looking for.
I recently found those explanatory videos that are quite helpful. in the same series there is a DeSeq2 tutorial
edit: fixed wrong links and description