HI Gordon,

Thanks. Does that mean in the second case, basically logFC = log2 (
 (average CPM in D+ average CPM in A) / (average
CPM in B +average CPM in C) ), except for other adjustments from negative
binomial?

Thanks,
Xinwei


On Tue, Apr 2, 2013 at 7:03 PM, Gordon K Smyth <smyth@wehi.edu.au> wrote:

> 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@duke.edu>
>> To: <bioconductor@stat.math.ethz.**ch <bioconductor@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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