[BioC] Select an affybatch subset prior to normalization

Javier Pérez Florido jpflorido at gmail.com
Mon Jan 26 09:47:32 CET 2009

Hi everyone,
I would like to perform the normalization process to a subset of 
interesting genes in the affybatch object. I know that "rma" function 
provides a parameter called "subset" to specify a list of probesets to 
restrict to for all calculations (the other probesets and their probe 
intensities are ignored).
But I would like to select a subset of data for vsnrma or expresso, 
which haven't got such parameter.
I've checked the bioconductor list and read something about modify the 
cdf environment, so, I've tried to do this (for Dilution experiment):

data(Dilution) #Get Dilution data
cleancdfname("HG_U95Av2") #Get hgu95av2cdf
difference=setdiff(ls(hgu95av2cdf),interestingGenes) #Get all genes that 
are not in the interesting genes set
rm(list=difference, envir=hgu95av2cdf) #Remove the genes for the cdf 
environment -> the cdf will have only the interesting genes
data(Dilution) #Get again the data with the updated CDF -> Dilution will 
have only the interesting genes
eset<-vsnrma(Dilution) #Performs normalization using only the 
interesting genes
detach("package:hgu95av2cdf") # Remove the modified cdf

BUT, after this code,  I try to get again the original data:
data(Dilution) #Get Dilution data
cleancdfname("HG_U95Av2") #Get hgu95av2cdf

The following error comes up:
Error in as.environment(pos): no item "hgu95av2cdf" in the search list

My code is in a for loop and I would like to modify the cdf in each 
iteration to select a different subset of data each time.

Any tips?
Thanks for your help,

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