Hi Jenny, We do this all the time. Simply subset the fit object that you give to topTable() or decideTests(), eg. topTable(fit[indicesofinterest,]) It is not usually necessary or desirable to subset before the eBayes() step, because that is intended to be whole-genome calculation. Best wishes Gordon > Message: 8 > Date: Thu, 24 Jul 2008 10:14:33 -0500 > From: Jenny Drnevich <drnevich at="" illinois.edu=""> > Subject: [BioC] how to test for genes of interest? > To: bioconductor at stat.math.ethz.ch > > Hi everyone, > > I've always heard that one of the ways "around" the multiple testing > problem of microarrays is for you to a priori identify a particular > list of genes you're interested in, and then you only have to do the > multiple test correction for this smaller list. I've never done this > in practice, and I'm not sure at what point in the analysis it's > proper to pull out just the smaller list. Obviously, all the data > preprocessing and normalization will be done with all the genes, but > should I pull out the genes before fitting the model, or after > fitting the model right before the multiple test adjustment? I'm > using the eBayes() shrinkage in limma, so which genes are in the > model will make a big difference in the outcome. > > I'm thinking it would be best to keep all the genes in the model, and > then split them out into two groups (genes of interest and all the > rest) and do a FDR correction separately for each group. What do you think? > > Thanks, > Jenny > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at illinois.edu