[BioC] User-defined genes in limma

[Jenny Drnevich]

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
>
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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

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1201 W. Gregory Dr.
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e-mail: drnevich at uiuc.edu