[BioC] parameterization or contrast matrix?

[bzzandrew at interfree.it]

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 

 
Andrea Bozzato, PhD Student 
Dip. Scienze Biomediche e Biotecnologie
Sez. Biologia e genetica
V.le Europa, 11
25123 Brescia 
ITALY
 
 

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