[BioC] filtered CDF file results in errors
seb at gerega.net
Fri May 2 01:48:12 CEST 2008
I am working on the yeast2 affymetrix chip and am trying to filter out
all the s_pombe probes with the following code:
bothcdf = wrapCdfEnvAffy(yeast2cdf, 496, 496, "yeast2cdf")
pp = read.table("s_pombe.msk", sep="\t", skip=2)
ids = as.character(pp[,1])
saccdf = bothcdf[ids]
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
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
What could be going wrong? Can anyone give me some tips to troubleshoot
thanks in advance,
I have tried again using the new BioC release and no longer get an error when creating the histogram.
However, now when I run fitPLM on the AffyBatch object R completely crashes. If I run fitPLM on the AffyBatch without having changed the CDF environment I get no problems.
Does anyone have any ideas what might be causing this? or how I could deal with the problem?
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