Dear all,

I am using limma for the analysis of a factorial experiment for the first time.
I would greatly appreciate your help re to few questions that I could not 
understand.
 
The experiment is 2^3 factorial, all the 3 factors at 2 levels each. 
I have 24 samples. The 3 factors ar below, it is a balanced design
genotype<-rep(c(1,2),each=12) ##here 2 represents RAG samples and 1 are WT
notch<-rep(rep(1:2,each=2),6)##Here 2 represents DL4 and 1 is OP9
trt<-rep(rep(1:2,2),6)##here 2 represents IL7 treated, while 1 is untreated
I define my design matrix as
 
design <- model.matrix(~factor(trt)*factor(notch)*factor(genotype))

The experimenters are interested in genes that are DE for the main effects and 
the co-regulation of those effects. So I do not define any contrast matrix, is 
that correct? What I mean to ask is that coefficients estimated by design matrix 
would suufice the objectives?
 
 Thanks a lot for your help 
 
Sincerely,
Shaheena


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