[BioC] filtered CDF file results in errors

[Sebastien Gerega]

Sebastien Gerega wrote:
> 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
>
>
> 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?
> thanks,
> Seb
>
>
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]
print(bothcdf)
print(saccdf)
saccdf at envName = "Sac ids only"
envsaccdf = as(saccdf, "environment")

However, I am still curious what was causing the problem....