[BioC] User-defined genes in limma

[Heather Erika Hallen]

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