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 ------------------------------------------------------------ Sei stanco di girare a vuoto? Con il nuovo motore di ricerca Interfree trovi di tutto. Vieni a trovarci: http://search.interfree.it/

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 > > >------------------------------------------------------------ >Sei stanco di girare a vuoto? >Con il nuovo motore di ricerca Interfree trovi di tutto. >Vieni a trovarci: http://search.interfree.it/ > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor 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