Thanks Ryan,

so lrt <- glmLRT(fit,contrast=c(1,-0.5-,-0.5),design) will override the
default coef  and coef is no longer required to be specified?

Regards,
Al


On Mon, Dec 10, 2012 at 8:50 PM, Ryan C. Thompson <rct@thompsonclan.org>wrote:

> 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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