[BioC] Factorial design with two-channel microarray data with Limma

[Eran Tauber]

Dear Gordon, 

Many thanks for your prompt reply. The User Guide and section 8.1.1 describes 
a simple comparison between two strains hibridized to the same array. In my 
experiment there are two factors, strain and treatment where for each strain, 
the two treatment were hybridized to the same array (see original post). My 
understanding was that my case resembles more example 8.7 in the manual, and 
my goal is to identify the genes that respond differently in one strain 
compared to the other (the interaction term, following the manual, question 3, 
p.44). The problem is that section 8.7 demonstrates it with Affymetrix data 
and I'm not sure how to apply it to a 2-channel experiment. Please advise, Eran