Re: limma - special case of contrasting

Assuming that your design matrix has columns C1.A, C2.A, C1.B, and 
C2.B, wouldn't the contrast simply be "C1.A - (C1.B+C2.A+C2.B)/3"? I.e. 
"C1.A minus mean of everything else". If your design matrix has an 
intercept column, it might be a little trickier to define that 
contrast, but still possible. You might just want to redo your design 
matrix to have the above columns and no intercept by doing "design <- 
model.matrix(~0 + celltype * treatment + donor, data=targets)", as 
recommended in the user's guide.

I think this gives you what you're looking for.

Hope this helps,
-Ryan

On Sun 09 Dec 2012 11:01:04 AM PST, Mitja Mitrovic wrote:
> Dear Gordon!
>
> sorry for being unclear. A and B are two distinct cell-surface proteins,
> whereas C1 and C2 are two different cell types, that were exposed to those
> treatments. Therefore I'd like to extract DEGs between cells with cell type
> C1 and expressing protein A (C1.A) and the rest of the cell populations
> (i.e. the combinations C1.B, C2.A and C2.B). Additionally, I have to
> control for the fact that in most instances cells were derived from the
> same donor. Do you see a straight forward way of getting the afore
> mentioned DEGs?
>
> Kind regards,
>
> Mitja
>
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>
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