Hello, all. I have a time course with six time points at 3-5 replicates per time point (total of 23 Affymetrix GeneChips). I would like to use limma to do comparisons between time points. I would like to normalize everything (all 18,000 probesets) with RMA, but then only examine the 180 genes involved in ion transport. These are custom affy chips, and not sufficiently annotated for me to use GO, but I know which genes I care about. I can readily generate the list with expression values using Ion <- exprs(eset)[c(234,17172,1006...), ], but don't know how to get this to interface with limma. Is this doable? Is there some other way to go about this (aside from normalizing only those genes)? Much thanks. Heather E. Hallen Research Associate Department of Plant Biology 166 Plant Biology Laboratories Michigan State University East Lansing, MI 48824-1312 USA

Hi Heather, The entire exprSet is subsettable using either row & column names or numbers. Just do this and Ion will be an exprSet you can use in limma: Ion <- eset[c(234,17172,1006...), ] Cheers, Jenny At 02:19 PM 5/24/2006, Heather Erika Hallen wrote: >Hello, all. > >I have a time course with six time points at 3-5 replicates per time point >(total of 23 Affymetrix GeneChips). I would like to use limma to do >comparisons between time points. I would like to normalize everything (all >18,000 probesets) with RMA, but then only examine the 180 genes involved in >ion transport. These are custom affy chips, and not sufficiently annotated >for me to use GO, but I know which genes I care about. I can readily >generate the list with expression values using Ion <- >exprs(eset)[c(234,17172,1006...), ], but don't know how to get this to >interface with limma. Is this doable? Is there some other way to go about >this (aside from normalizing only those genes)? > >Much thanks. > > >Heather E. Hallen >Research Associate >Department of Plant Biology >166 Plant Biology Laboratories >Michigan State University >East Lansing, MI 48824-1312 USA > >_______________________________________________ >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 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 uiuc.edu