[BioC] A doubt with contrasts in limma

[Cittaro Davide]

Hi all,
If I have a 2x2 design (gen[AB], treat[CD]), I've created a design matrix so that I have 4 classes: A.C, A.D, B.C and B.D. Now I'm interested in finding the global differences between genA and genB, the global differences between treatC and treatD and their interaction, is it correct to specify contrasts like:

(A.C + A.D) - (B.C + B.D) for genotypes
(A.C + B.C) - (A.D + B.D) for treatments
(A.C - A.D) - (B.C - B-D) for interactions (as in the manual)

?

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