[BioC] Limma or something else ? plus Normalization
smyth at wehi.edu.au
Mon Sep 29 12:16:26 MEST 2003
At 02:47 AM 29/09/2003, Phguardiol at aol.com wrote:
>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
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