[BioC] problems in makecdfenv with affy custom resequencing arrays

[Vishal Berry]

I am trying to analysing data from Affymetrix CustomSeq Resequencing Arrays with bioconductor and am having trouble with the CDF file.  This is a custom chip so the package is not available, but I have the affy CDF file.  

I have tried to create a CDF package using the instructions in the "Textual Description of makecdfenv" utilizing make.cdf.package().  I have also unsuccesfully tried to make an environment with make.cdf.env().  Running both gives me a "Program Error: Rgui.exe has generated errors and will be closed".  I have also tried the non-gui R (still in win2k) and get the same error.  

I'm running R 1.9.1,  Bioconductor 1.4, MinGW 3.1.0, Win2k.  Has anyone been able to create cdf enviornments for affy custom reseq. arrays?  Previous posts have enumerated problems installing manually created cdf packages, but I cant create env from my cdf file (so of course no packages either).  

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Vishal Berry
vrb at andrew.cmu.edu
Bioinformatics
Cincinnati Children's Hosptial Medical Center