[BioC] filtered CDF file results in errors
seb at gerega.net
Fri May 2 02:24:33 CEST 2008
Sebastien Gerega wrote:
> 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 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,
> 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?
I seem to have resolved this problem by removing the probes listed in
"s_cerevisiae.msk" rather than using those listed in "s_pombe.msk" with
the following code:
bothcdf = wrapCdfEnvAffy(yeast2cdf, 496, 496, "yeast2cdf")
pp = read.table("s_cerevisiae.msk", sep="\t", skip=2)
ids = geneNames(bothcdf)[which(geneNames(bothcdf) %in% pp[,1] == FALSE)]
saccdf = bothcdf[ids]
saccdf at envName = "Sac ids only"
envsaccdf = as(saccdf, "environment")
However, I am still curious what was causing the problem....
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