[BioC] limma factorial designs with technical replicates

[Jianping Jin]

Dear list:

I am working on a small data set that came from cytokine membranes. Each 
membrane contains 23 specific cDNA fragments spotted in duplicates. The 
experiment design includes two treatment of interest, stimulant 
(pre-activated or non-activated cells)  and inhibitor (w/ or w/o 
inhibitor).  After manual normalization based on control spots on each 
membrane, I like to run limma as factorial design. My question is how I 
should handle the duplicate spots (block effect) in limma processing?

Thanks!

JP-