Hi, 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 Philippe

At 02:47 AM 29/09/2003, Phguardiol@aol.com wrote: >Hi, >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, Please explain what LPE is. > 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 >Philippe