[BioC] limma: results from different coefficients

[kfbargad at ehu.es]

Dear list,

I have three groups of samples (Tto, NoTto, C) and have made the three 
possible pairwise contrasts as follows:

design.tto <- model.matrix(~-1+factor(c
(1,1,2,2,2,3,2,1,3,1,2,2,3,1,1,2,1,1,3,1)))
colnames(design.tto) <- c("C","Tto", "NoTto")

fit.tto <- lmFit(eset,design.tto)
contrast.matrix.tto <- makeContrasts(Tto-C,NoTto-C, Tto-NoTto, levels 
= design.tto)
fit2.tto <- contrasts.fit(fit.tto, contrast.matrix.tto)
fit3.tto <-eBayes(fit2.tto)

If I select all d.e (p<0.05) genes from each contrast of interest I 
get the same number of genes, 463, although different

topTable(fit3.tto, coef = X(where X =1,2 or 3)#, adjust="none", 
sort.by="P", number=5506); NoTto_vs_C_y <- NoTto_vs_C[x$P.Value < 
0.05,]

dim(Tto_vs_C_y)
[1] 463   7
> dim(NoTto_vs_C_y)
[1] 463   7
> dim(Tto_vs_NoTto_y)
[1] 463   7


Is this normal?

Thanks in advance

David