[BioC] logFC and CPM of edgeR

Shuhei Yao [guest] guest at bioconductor.org
Fri Apr 18 11:09:01 CEST 2014

Hi, All.

Let me confirm my understandings about logFC and CPM of edgeR.

1."logFC" using glm functions are calculated from normalized factor. This process does not include transformation to cpm.
2. CPM should be calculated from count with its normalized factor, Main purpose of cpm to show heatmap (is described in User's guide).

'logFC' from cpm are different from 'logFC' using glm functions. I'm sure that this result is general according to my understanding. Is it correct ? And which count data (e.x. cpm, pseudo count and fpkm) is suitable for pharmacologist ?   


 -- output of sessionInfo(): 

> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)


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