[BioC] limma contrasts

renns renns at reed.edu
Thu Jul 24 21:11:04 CEST 2008

I have a loop design experiment in which I compare two types of males 
and females. There are 6 individuals in each group. For the pairwise 
comparison I build the contrasts with the following:

design_NT1 <- modelMatrix(targets, ref = "NT1")
contrasts <- makeContrasts (NvsT = 
(NT2+NT3+NT4+NT5+NT6-T1-T2-T3-T4-T5-T6)/6, FvsN = 
(F1+F2+F3+F4+F5+F6-NT2-NT3-NT4-NT5-NT6)/6, TvsF = 
(T1+T2+T3+T4+T5+T6-F1-F2-F3-F4-F5-F6)/6, levels = design_NT1)

Now i want to extract the difference between all males (regardless of 
type) and females, but I'm not sure how to do this?


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