[BioC] extracting one probe set

James W. MacDonald jmacdon at med.umich.edu
Mon Aug 23 23:02:46 CEST 2004

Thomas Turner wrote:

> Dear all,
> I am trying to simply extract a table with the probe intensities for a 
> probe set that I specify by name.  As described in 6.2 of the manual, I 
> have been trying to use this command:
> ps <- probeset(affybatch, genenames = ("probe set name"))

Probably an easier method is to simply use the pm() and mm() accessor 

pm(affybatch, genename)
mm(affybatch, genename)



> However, I am unable to make the following command work: 
> pm(ps[[1]]) 
> If I ask R about my "ps", it gives me this:
> $"Ag.X.66.0 CDS s at"
> ProbeSet object:
>   id=Ag.X.66.0 CDS s at
>   pm= 1 probes x  1  chips
> My affybatch includes four chips, which do not seem to be what this is 
> telling me.  I am new to R, and any advice would be warmly received.
> Thank you,
> Tom Turner
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James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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