[BioC] reference design

[Naomi Altman]

Each of your arrays has M=S-R  where S is one of Mut1 or Mut2 and R 
is reference.
(Mut1-R)-(Mut2-R)=Mut1-Mut2.

So, the contrast will do what you want, and the M values from limma 
are line 2 above.

--Naomi

p.s. Just trying to save Gordon some time.


At 05:19 AM 5/5/2006, bzzandrew at interfree.it wrote:

>Dear Gordon,
>i performed 8 technical replicates with two color oligo array. 
>Particularly i have 3 samples: MUT1, MUT2 and Reference (pool of 
>wild type mice), then my experiments were MUT1 vs REFERENCE 
>(4replicates with 2 dye swap) and the same for MUT2 (MUT2 vs 
>REFERENCE). Then i analyzed with genepix and with limma or limmaGUI. 
>My question is: can i perform a comparison etween MUT1 vs MUT2 using 
>a parameterization MUT1 minus MUT2? If i do this, how thw M values 
>are computed? or is it better compute a contrast matrix??
>thanks a lot
>
>andrea
>
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111