[BioC] Limma or something else ? plus Normalization question

Phguardiol at aol.com Phguardiol at aol.com
Sun Sep 28 13:47:32 MEST 2003

let say I have 9 chips (Affy U133A) 
A1, A2, A3  triplicates = group A
B1, B2, B3  triplicates = group B
C1, C2, C3  triplicates = group C

I d like to know what are the genes differentially expressed between A & B, A & C, B & C
I see two options (1) comparing 2 by 2 these groups using for instance LPE or another test like this one, option (2) using Limma. 
What would be the best option ? I like using LPE since it is well designed for low replicates. If I  use option (1) should I normalize all the chips during the same process or first normalize group A with group B and run the comparison..etc ? My concern here is that I will use a relatively low number of chips with RMA / Quantile normalization, in the other way (normalizing everything at the same time) I could introduce "a bias" that is not needed. 
Any comments is apppreciated as usual.Thanks

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