Justine Peeters wrote: > Hello, > > I was wondering if there were any R packages as yet for analysing 100K Affy > SNP chips specifically for linkage/autozygosity? Is there anyone who has > experience in analysing 100K SNP chips? Not yet, but we are working on it. The existing infrastructure for handling raw Affy data are not amenable to the new SNP chips, so we need both a package to handle the raw data as well as a package with the methods to analyze. We are still in the preliminary stages, but hopefully will have something useful this Summer. In the interim, Affy's GCOS will do the linkage and SNP calls, and they also have a copy number tool if you are interested in additions/deletions. Best, Jim > > Regards, Justine > > > > Justine Peeters > > Bioinformatician > > > > Department of Bioinformatics > > ErasmusMC > > Postbus 1738, 3000DR > > Rotterdam, Netherlands > > Kamer Ee15.38a > > > > +31 624668045 > > > > > > > > > [[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 734-647-5623