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Old 08-19-2014, 02:49 PM   #10
feralBiologist
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Quote:
Originally Posted by dpryan View Post
CPM isn't used to calculate differential expression, so it doesn't fit your definition of normalization (normalization is a generic term that doesn't really fit what you wrote). Nothing in Gordon's reply contradicts James' a reply on the mailing list.
Thanks for your response but it still does not clarify the question I asked. OK, let's drop "normalisation" as it is a confusing term. What I really wanted to know is "How do you come from raw counts to cpm()'s output? What are the transformations/manipulations performed?"

One thing mentioned by Gordon Smyth is the library size scaling. Is this all? I had a look at the help info on cpm() - it does not explicitly mention anything else.
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