Can bioconductor read binary CDF/CEL files? I am trying to use make.cdf.package to create an environment for 100k SNP arrays. Thanks, Neil [[alternative HTML version deleted]]

Christopher, Neil (NIH/NCI) wrote: > Can bioconductor read binary CDF/CEL files? I am trying to use > make.cdf.package to create an environment for 100k SNP arrays. No for CDF and yes for CEL. Ben Bolstad is working on the CDF files and should have something in December. I made a cdfenv for what Affy was calling the CenthindAv2.cdf, which appears to now be called the Mapping50k_hind.cdf, back when it was still a text file. Unfortunately, the IDs appear to have changed in the interim because they don't agree with what Affy supplies in their annotation file. I would offer this cdfenv to you, but as I mentioned, it doesn't appear to agree with the current identifiers so I am not sure how useful it is. Best, Jim > > > > Thanks, > > > > Neil > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@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

I thought gcrma has a facility to read the binaries. Peter At 11:08 AM 11/16/2004, Christopher, Neil (NIH/NCI) wrote: >Can bioconductor read binary CDF/CEL files? I am trying to use >make.cdf.package to create an environment for 100k SNP arrays. > > > >Thanks, > > > >Neil > > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor

I believe it can read CEL binaries. But in order to make each chip environment, you need to read the CDF files. Neil -----Original Message----- From: Pita [mailto:pwilkinson_m@xbioinformatics.org] Sent: Tuesday, November 16, 2004 11:48 AM To: Christopher, Neil (NIH/NCI); bioconductor@stat.math.ethz.ch Subject: Re: [BioC] Binary CDF and CEL files I thought gcrma has a facility to read the binaries. Peter At 11:08 AM 11/16/2004, Christopher, Neil (NIH/NCI) wrote: >Can bioconductor read binary CDF/CEL files? I am trying to use >make.cdf.package to create an environment for 100k SNP arrays. > > > >Thanks, > > > >Neil > > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor