[BioC] User-defined genes in limma
Heather Erika Hallen
hallenhe at msu.edu
Wed May 24 21:19:22 CEST 2006
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
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