[BioC] Limma or something else ? plus Normalization question

[Gordon Smyth]

At 02:47 AM 29/09/2003, Phguardiol at 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