Dear members,
 
I'm struggling to create the contrast matrix for our experiment comprising of 4 genotypes in treated and untreated conditions:
 
The genotypes are labelled C1 to C4
The conditions are treated (F) and untreated (M)
I set up the contrast matrix like this:
 
cont.matrix.30 <- makeContrasts(
C1_FvsM=C1F-C1M,
C2_FvsM=C2F-C2M,
C3_FvsM=C3F-C3M,
C4_FvsM=C4F-C4M,
Diff_C1C2=(C1F-C1M)-(C2F-C2M),
levels=design)
 
 
The first four "normal" contrasts estimating the response of treated/untreated genotypes are working great. My problem is the "double contrast" Diff_C1C2 where I want to find those genes that show a difference in response (treated vs untreated)  between the two genotypes C1 and C2.
 
 
I would gladly accept any help!
 
Thanks
Christian
 
 
 
 
 

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