[BioC] how to handle pooled replicate?

[Jianping Jin]

Dear list:

There is a data set, consisting of 3 Agilent slides. The experiment was run 
with direct hybridization, knock-out versus wild-type, and no dye swap. Due 
to difficulty of collecting samples, the samples were pooled and hybridized 
onto 3 separate slides.

Of course the 3 slides are not biological replicates. They are not pure 
technical replicates either. How should I set up a design matrix for limma 
model analysis?

Thanks!

JP-

##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
CB# 7104
University of Chapel Hill
Chapel Hill, NC 27599
Phone: (919)843-6105
FAX:   (919)843-3103
E-Mail: jjin at email.unc.edu