After loading the data package for mgu74a, ls(mgu74aCHRLOC) will list all the probe ids, get("aProbeId", mgu74aCHRLOC) will get you the chromosomal location for "aProbeId", and multiget("probeIds", mgu74aCHRLOC) will return a list containing chromosomal location data for "probeIds". Chromosomal locations are named by the chromosome number. Built in information about data packages can be obtained by typing packageName(), ?packageName, and ?dataSetName (e.g. mgu74a(), ?mgu74a, and ?mgu74aCHRLOC) after loading a data package. >Date: Mon, 28 Apr 2003 17:24:26 -0700 (PDT) >From: Jeffrey Rasmussen <rasmuss@u.washington.edu> >To: bioconductor@stat.math.ethz.ch >Subject: [bioC] GenePlotter for mgu74v2 >MIME-Version: 1.0 >X-Virus-Scanned: by amavisd-milter (http://amavis.org/) >X-Virus-Scanned: by amavisd-milter (http://amavis.org/) >X-Spam-Status: No, hits=-3.3 required=5.0 tests=IN_REP_TO version=2.53 >X-Spam-Level: >X-Spam-Checker-Version: SpamAssassin 2.53 (1.174.2.15-2003-03-30-exp) >X-BeenThere: bioconductor@stat.math.ethz.ch >X-Mailman-Version: 2.1.1 >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >List-Help: <mailto:bioconductor- request@stat.math.ethz.ch?subject="help"> >List-Post: <mailto:bioconductor@stat.math.ethz.ch> >List-Subscribe: <https: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=subscribe> >List-Archive: <https: www.stat.math.ethz.ch="" pipermail="" bioconductor=""> >List-Unsubscribe: <https: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=unsubscribe> > >Hi. > >Has anyone used the GenePlotter package on the mgu74Av2 affymetrix array? >I have been unable to figure out how to extract the chromosomal >location for the probesets from the data package for the u74 chip. Is this >information built into that data package? If not, could someone please >point me to how one might go about compiling the required data? > >Thanks! >Jeff. > >__________________________________ >Jeffrey Rasmussen >Research Consultant, Bioinformatics >Department of Immunology >University of Washington > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

Hi Jeff, Did you make any progress? There were some minor glitches in the devel version of geneplotter (that have now been repaired) so that the byChroms HowTo should once again be available. This document details the steps needed to construct the basic object you need to use the geneplotter package. library(DynDoc) openVignette("geneplotter") should give you an menu, from that you can select the byChrom vignette (on windows this should appear in the menu bar but that is slightly broken -- look for a new R release in the next few days), You can also extract the code from the vignette by using tangleToR (also in the DynDoc package), and of course there is always vExplorer for a more interactive tool for looking at the code, (it is in the package tkWidgets), please let me know if you need more details Robert On Mon, Apr 28, 2003 at 05:24:26PM -0700, Jeffrey Rasmussen wrote: > Hi. > > Has anyone used the GenePlotter package on the mgu74Av2 affymetrix array? > I have been unable to figure out how to extract the chromosomal > location for the probesets from the data package for the u74 chip. Is this > information built into that data package? If not, could someone please > point me to how one might go about compiling the required data? > > Thanks! > Jeff. > > __________________________________ > Jeffrey Rasmussen > Research Consultant, Bioinformatics > Department of Immunology > University of Washington > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+