[BioC] logFC in GLM of egdeR

[Gordon K Smyth]

Dear Xinwei,

Well, in the first case you get C-A (C minus A).  In the second case you 
get A-B-C+D.

Best wishes
Gordon

> Date: Mon, 1 Apr 2013 23:10:42 -0400
> From: Xinwei Han <xinwei.han at duke.edu>
> To: <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] logFC in GLM of egdeR
>
> Hi,
>
> I fit a GLM with edgeR like this:
>
>> colnames(fit)
> A B C D
>
> For contrast = c(-1,0,1,0), I guess logFC = log2 (average CPM in C/ average
> CPM in A).
>
> But for contrast = c(1,-1,-1,1), how is logFC calculated?
>
> Thanks,
> Xinwei
>

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