reference design
1
0
Entering edit mode
@bzzandrewinterfreeit-1710
Last seen 7.2 years ago
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/
limma limmaGUI oligo limma limmaGUI oligo • 635 views
ADD COMMENT
0
Entering edit mode
Naomi Altman ★ 6.0k
@naomi-altman-380
Last seen 6 months ago
United States
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
ADD COMMENT

Login before adding your answer.

Traffic: 433 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6