[BioC] limma and makeContrasts

[Stephen Henderson]

Hi
I've been using the limma and eBayes function for looking at a set of
affymetrix chips with 8 or so different groups within. Following the
instructions on page 11=12 of the PDF guide, this works fine I think.  

My question regards different ways to specify the contrasts. If I wish to
compare composite groups, e.g.

(group1,group2) vs (group3,group4) and others

is there a syntax to specify this within the makeContrasts function?, and
where can I read about this?, or alternatively is there a better step at
which I can achieve this (without changing my class vector repeatedly that
is)? 

Stephen


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