[BioC] filtered CDF file results in errors

[Sebastien Gerega]

Hi,
I am working on the yeast2 affymetrix chip and am trying to filter out 
all the s_pombe probes with the following code:

library(altcdfenvs)
bothcdf = wrapCdfEnvAffy(yeast2cdf, 496, 496, "yeast2cdf")
pp = read.table("s_pombe.msk", sep="\t", skip=2)
ids = as.character(pp[,1])
saccdf = bothcdf[ids]
print(bothcdf)
print(saccdf)
saccdf at envName = "Sac ids only"
envsaccdf = as(saccdf, "environment")
data = ReadAffy(filenames=filenames)
data at cdfName <- "envsaccdf"

"s_pombe.msk" was downloaded from the Affymetrix website and contains a 
list of all the s_cerevisiae probes (those I want to use).

This code runs without problems but once I get to QC I get the following 
error:
hist(data, main="Log2(Intensity)", col=targetCol)
Error in density.default(newX[, i], ...) : 'x' contains missing values

I have tried running the reverse analysis, that is filtering out the 
s_cerevisiae probes instead of the s_pombe ones and I no longer get the 
error.
What could be going wrong? Can anyone give me some tips to troubleshoot 
the problem?
thanks in advance,
Seb