[BioC] Replace method, AffyBatch, pm or mm

[James W. MacDonald]

laurent buffat wrote:
> 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

No I can't. As Rafael noted, the "pm<-" method only allows for the 
replacement of all the pm probes in a given AffyBatch. I'm curious 
though; why do you want to replace pm values rather than filtering, etc 
at the expression value stage? NA values appear to cause problems with 
some of the processing steps for e.g., rma.

> 
> 
> Is it working for you ?
> 
> Thanks for your help.
> 
> Laurent Buffat.

-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109