I have been using SAM to estimate FDR when performing multiple comparisons on two groups. I have now been tasked with performing a similar analysis on a 2X2 experiment (2 groups each with two treatments). For a single comparison, ANOVA would be the obvious choice. What should be my approach for multiple (about a thousand) comparisons? Thanks, Mark W. Kimpel MD (317) 490-5129 Home, Work, & Mobile (317) 278-4104 FAX

I would use limma followed by qvalue (another Bioconductor package). There are several examples on this mainling list of how to set this up. Check my message of yesterday for a comment about the correspondance between SAM and limma for 1-way ANOVA. -Naomi At 10:28 AM 6/25/2004 -0500, Kimpel, Mark W wrote: >I have been using SAM to estimate FDR when performing multiple >comparisons on two groups. I have now been tasked with performing a >similar analysis on a 2X2 experiment (2 groups each with two >treatments). For a single comparison, ANOVA would be the obvious choice. >What should be my approach for multiple (about a thousand) comparisons? > >Thanks, > >Mark W. Kimpel MD > > > >(317) 490-5129 Home, Work, & Mobile > >(317) 278-4104 FAX > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Bioinformatics Consulting Center Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111