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Old 08-18-2014, 03:03 AM   #6
Location: UK

Join Date: Jun 2011
Posts: 61

A search suggests that you have posted three questions to the Bioconductor mailing list, and that I have answered all of them myself.
You are right - and I once again thank you for this. I will not post edgeR questions to seqanswers anymore. In the past I have used seqanswers a lot more often than I have used bioconductor (and not just for edgeR) and not all of my questions have been answered. Quick search in seqanswers shows this. Maybe some of them were not precisely formulated - I don't know. But they made me think that help might not always come.
But your cross post of James MacDonald's answer isn't correct.
This is how I understood the answer of James. He says that counts are not affected by the normalization and I explained on the bioconductor thread that I understood "normalisation" to comprise all the transformations performed on the raw counts. Thanks to your kind reply in bioconductor I was reminded that in edgeR "normalisation" refers to multiple transformations and that not all of them are reflected in the cpm() output. I was about to post this clarification but you were faster than me.

Once more - thanks again for your assistance and for helping to create edgeR and other analytic tools that I have used.
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