[BioC] eset -Affy Mouse Gene 1.0 ST. Array-

[James W. MacDonald]

Hi Alessandro,

On 5/10/2012 6:39 AM, alessandro brozzi wrote:
> hi all,
> I'm working on Affy Mouse Gene 1.0 ST. Array.
>
> If I do:
>
> rawData = ReadAffy()
> eset = rma(rawData)
>
> I end up with 34760 Features which correspond to transcript_cluster_id.
> Each transcript_cluster_id is formed by several probe_ids
>
> How can I make an eset with the probe_id levels not summarized in
> transcript_cluster
> s?

Don't use the affy package.

library(oligo)
rawData <- read.celfiles(list.celfiles())
eset <- rma(rawData, target = "probeset")

This will summarize at the probeset level, which is roughly the exon 
level (some probesets span multiple exons).

Best,

Jim


>
> thanks in advance,
> Alex
> *
> -----------------------------
> Alessandro Brozzi, PhD
> Department of Mathematics
> University of Perugia,
> Via Vanvitelli 1, 06123 Perugia, Italy
> tel: + 39 075 585 5039
> fax: **+ 39 075 585 5024
> *
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099