[BioC] limma and block effect

Wenbin Liu wnbnl at yahoo.com
Tue Aug 16 00:30:34 CEST 2005


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



More information about the Bioconductor mailing list