Hi, For the Affy 6.0 platform, I would like to know the default tool for obtaining copy number estimates prior to smoothing across loci (raw copy number). If CNAT is the default, is there a command-line version of this tool available, or an implementation of a CNAT- equivalent in R? Thanks, Rob

Have a look at aroma.affymetrix http://www.braju.com/R/aroma.affymetrix/ There is a vignette illustrating how you can get raw copy-number estimates on GenomeWideSNP_6 (GWS6) (and all other Affymetrix SNP/CN platforms). The CNAT method/algorithm does not apply to the GWS5/6 chip types - only 500K and before. For Affymetrix solutions, have a look at Affymetrix Power Tools (APT), which is an open-source cross-platform command line based set of methods. FYI, the Affymetrix Genotype Console (GTC) analyzes GWS6 and is a Windows GUI that utilizes APT for its processing (according to the docs of the latest release; it is no longer relying on Matlab binaries). Cheers Henrik On Tue, Aug 5, 2008 at 7:29 PM, Rob Scharpf <rscharpf at="" jhsph.edu=""> wrote: > Hi, > > For the Affy 6.0 platform, I would like to know the default tool for > obtaining copy number estimates prior to smoothing across loci (raw copy > number). If CNAT is the default, is there a command-line version of this > tool available, or an implementation of a CNAT-equivalent in R? > > Thanks, > > Rob > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >