[BioC] limma voom: How to create double contrasts?

[James W. MacDonald]

Hi Christian,

On 7/17/2012 4:32 AM, Christian Ametz wrote:
> Dear members,
>
> I'm struggling to create the contrast matrix for our experiment comprising of 4 genotypes in treated and untreated conditions:
>
> The genotypes are labelled C1 to C4
> The conditions are treated (F) and untreated (M)
> I set up the contrast matrix like this:
>
> cont.matrix.30<- makeContrasts(
> C1_FvsM=C1F-C1M,
> C2_FvsM=C2F-C2M,
> C3_FvsM=C3F-C3M,
> C4_FvsM=C4F-C4M,
> Diff_C1C2=(C1F-C1M)-(C2F-C2M),
> levels=design)
>
>
> The first four "normal" contrasts estimating the response of treated/untreated genotypes are working great. My problem is the "double contrast" Diff_C1C2 where I want to find those genes that show a difference in response (treated vs untreated)  between the two genotypes C1 and C2.

The technical term for that contrast is an interaction, and you have set 
it up correctly. So what is the problem?

Best,

Jim


>
>
> I would gladly accept any help!
>
> Thanks
> Christian
>
>
>
>
>
>
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099