Dear limma users, I have an experiment designed as follows: Samples were taken from 3 individuals(S1, S2 and S3), and for the sample from each individual, there are four treatments (A,B, C, and D). Each sample was hybridized to an Affymetrix expression array. Therefore, the individuals serve as blocks. Will the following code work? treat <- as.factor(rep(c("A", "B", "C", "D"), 3)) block <- rep(1:3, rep(4,3)) design <- model.matrix(~ -1 + treat) fit1 <- lmFit(dat, design=design, block=block) # where dat is an ExprSet. In addition, what if I have a missing chip (11 chips instead of the balanced 12 ones)? Will argument method='gls' do the job? Any comment or hint will be greatly appreciated! Wenbin