[BioC] Replace method, AffyBatch, pm or mm

[laurent buffat]

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