[BioC] specifying contrast in edgeR

[Ryan C. Thompson]

glmFit doesn't take a contrast argument as far as I know. You only 
specify the contrast in glmLRT.

On Mon 10 Dec 2012 06:47:40 PM PST, Alpesh Querer wrote:
> Hi all,
>
> I want to test the hypothesis Cond1-(Cond2+Cond3)/2 =0 in glmFIT, do I need
> to specify (1,-0.5,-0.5) as the contrast vector in glmFit?
> Also should I include this contrast in glmLRT as well or it automatically
> uses the contrast used in the previous step?
> Will the following commands give me what I want?
>
> fit <- glmFit(dgelist_object, design,contrast=c(1,-0.5-,-0.5))
> lrt <- glmLRT(fit)
>
> Thanks,
> Al
>
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