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). ******* Vishal Berry vrb@andrew.cmu.edu Bioinformatics Cincinnati Children's Hosptial Medical Center