[BioC] replicate arrays for limma

Simon Melov smelov at buckinstitute.org
Sun Dec 14 08:16:19 MET 2003

Im new to limma, and I'm trying to determine a design matrix for the 
following type of experiment. I dont see an example of this sort of 
experiment which is becoming increasingly common. I have Diseased vs 
control (two color). I have 30 diseased individuals, and each 
individual has had 4-6 technical replicates carried out with dye swaps 
involved. My question is, how to capitalize on the robustness of the 
technical reps per individual? Is there a way in limma of obtaining the 
least variable genes per technical rep set (which I guess violates 
independence somewhat as the 4-6 replicates are done on the same 
individual), and then comparing these results to all the other 29 
diseased individuals (who will have had the same filtering done to 
identify the most robust differentially expressed genes compared to the 
control). Ulimatley this will result in the identification of the most 
robustly differentially expressed genes across all 30 individuals, but 
will have capitalized on the fact that each individual was technically 
replicated between 4-6 times.

Maybe this is straightforward, but I cant figure out how to do it, 
please help!



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