I am trying to use the information in CDF files from the BioConductor website www.bioconductor.org/data/cdfenvs/cdfenvs.html) Although there are 287296 (536x536) probes on an hu6800 chip, I only get 281966 probes (from 7129 "genes") in the hu6800cdf data. I counted the probes for each "gene" and added to get a total of 281966. Am I missing duplicates? What am I doing wrong? My objective is to merge the CEL and CDF files so that I can perform my own analysis.

On Mon, Apr 21, 2003 at 02:07:07PM -0600, Ann Hess wrote: > I am trying to use the information in CDF files from the BioConductor > website www.bioconductor.org/data/cdfenvs/cdfenvs.html) > > Although there are 287296 (536x536) probes on an hu6800 chip, I only get > 281966 probes (from 7129 "genes") in the hu6800cdf data. I counted the > probes for each "gene" and added to get a total of 281966. > > Am I missing duplicates? What am I doing wrong? My objective is to merge > the CEL and CDF files so that I can perform my own analysis. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Not all the probes on a chip correspond to genes. Some are controls for (for gridding), some others are more mysterious to me.... I won't ask too many questions about your objectives, but I would trend to think that 'affy' and 'makecdfenv' would take care of the job for you. Hopin' it helps, L. -- -------------------------------------------------------------- currently at the National Yang-Ming University in Taipei, Taiwan -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent