[BioC] Replace method, AffyBatch, pm or mm
laurent buffat
laurent.buffat at it-omics.com
Wed Oct 20 15:43:19 CEST 2004
Hi James,
I'm using exactly the same Affy ProbeSet ids that you did in your example :
> library(affy)
> data(affybatch.example)
> pm(affybatch.example, geneNames(affybatch.example)[1])
Error in .local(object, which, ...) : couldn't find function "multiget"
But I don't have the same version of R (1.9.0) and affy (1.5.0)
I will reinstall completely R and bioconductor with the new version and try
this example again, but I have actually a solution with the intensity slot.
Are you able to replace the pm intensity ? If you do
> pm(dat, geneNames(dat)[1]) <- NA
Is it working for you ?
Thanks for your help.
Laurent Buffat.
-----Message d'origine-----
De : James W. MacDonald [mailto:jmacdon at med.umich.edu]
Envoye : mercredi 20 octobre 2004 15:26
A : laurent buffat
Cc : bioconductor at stat.math.ethz.ch; 'Robert Gentleman';
bioconductor at stat.math.ethz.ch
Objet : Re: [BioC] Replace method, AffyBatch, pm or mm
laurent buffat wrote:
>
> Hi,
>
> Thanks for Raphael, Robert & Laurent for your answers. It helps me to
solve
> my problem:
>
> I work with R 1.9.0 and affy 1.5.0, but:
>
> Historically, to get a probe intensity of a probe set name, I used an old
> "signature" of pm: pm( aBatch, aProbeSetName)
What exactly are you using for aProbeSetName? This still works for me
using R-2.0.0 and affy-1.5.6, if I use the Affy probe ids.
> pm(dat, geneNames(dat)[1])
001.CEL 002.CEL
1007_s_at1 268.3 781.0
1007_s_at2 310.0 1154.5
1007_s_at3 607.8 1576.0
1007_s_at4 2360.5 6501.0
1007_s_at5 1765.8 5157.3
1007_s_at6 1471.8 4359.5
1007_s_at7 474.5 1430.8
1007_s_at8 555.5 1559.8
1007_s_at9 196.5 646.5
1007_s_at10 1016.3 3987.0
1007_s_at11 1455.0 3440.3
1007_s_at12 1090.8 2439.8
1007_s_at13 1231.0 2697.0
1007_s_at14 201.0 498.8
1007_s_at15 520.3 1084.8
1007_s_at16 1494.3 3697.8
--
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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