I tried to generate a cdf packages with make.cdf.package for the Mapping50K chips. I got the error message that cdf packages can not be generated for this type of chips. Is there any other way to generate the cdf packages? Thanks Tim -------------------------------------------------------------- Tim M. Strom Tel: +49 89 3187 3296 Institut fuer Humangenetik Fax: +49 89 3187 3297 Ingolstaedter Landstr. 1 85764 Neuherberg Germany WWW: http://ihg.gsf.de

Tim Strom wrote: > I tried to generate a cdf packages with > make.cdf.package > for the Mapping50K chips. > I got the error message that cdf packages > can not be generated for this type of > chips. > > Is there any other way to generate > the cdf packages? Yes. The makePlatformDesign package in the devel repository has functionality to make these packages. You will need the cdf, the FASTA probe sequences, and the csv annotation file (all available on Affy's website). This package is still quite developmental - the only information about the functions is the comments in the code. In addition, there is only a source version available, so if you are on windows or MacOS, you will have to get set up to build source packages. In addition, these mapping cdfs are quite large. On a 64 bit OS with 16 Gb RAM, it only takes about 15 minutes to build the package. On my pitiful win32 box with 2 Gb of RAM I start swapping almost instantaneously, so I have to let it run overnight. The makePlatformDesign package is the next generation version of makecdfenv, and is designed to work with the oligo package (the next generation version of affy). Unfortunately, I have not had the time this Summer to add the basic accessor functions to oligo for the SNP chips, not to mention any higher level functionality, so simply building the PDenv for a given chip will not allow you to do any analyses without some further code writing. If you are looking for analysis tools that already exist, Affy's GDAS and copy number tool are one route, and I believe dChipSNP will now work with the 100K chips as well (I see a paper in last week's Nature where they use dChipSNP on 100K chips). HTH, Jim > > Thanks > Tim > > > -------------------------------------------------------------- > > Tim M. Strom Tel: +49 89 3187 3296 > Institut fuer Humangenetik Fax: +49 89 3187 3297 > Ingolstaedter Landstr. 1 > 85764 Neuherberg > Germany > > WWW: http://ihg.gsf.de > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623