[BioC] limma and block effect

[Wenbin Liu]

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