[BioC] Limma and multiple groups

[Andrew Beggs [guest]]

Hi,

I am analysing microarray experiments with two groups, and with 3/4 groups using limma.

I am looking at differential methylation between, for example, two groups with 3 samples in each, which I can easily do by setting my design matrix to say:

design <- cbind(Grp1=1,Grp2vs1=c(0,0,0,1,1,1))

How do I do this with say 3 (or even 4) groups, i.e. Early-Intermediate-Late disease states vs. methylation?

Many thanks for helping - sorry it's such a basic question.

Andrew

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