Hi all I have used affy to get perfect-match probe data for a number of affy HG-U133a chips and I get the probes as follows 210298_x_at1, 210298_x_at2 etc How do I find out what the mapping is to the oligodata that Affymetrix give for their probes as I want to know the position the oligos bind to in the sequence as this is a gene with an alt-splicing site? Look forward to your reply. Keith ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr J Keith Vass Bioinformatics Unit, Cancer Research UK Beatson Institute Garscube Estate Bearsden Glasgow G61 1BD eMail k.vass@beatson.gla.ac.uk FAX (44) (0)141 942 6521

i believe this information is available through the matchprobes package (available from http://www.bioconductor.org/repository/devel/package/html/index.html ) and the hgu133a probepackage (available here: http://www.bioconductor.org/data/metaData.html ) On Wed, 27 Aug 2003, Keith Vass wrote: > Hi all > > I have used affy to get perfect-match probe data for a number of affy > HG-U133a chips and I get the probes as follows 210298_x_at1, 210298_x_at2 > etc > > How do I find out what the mapping is to the oligodata that Affymetrix > give for their probes as I want to know the position the oligos bind to in > the sequence as this is a gene with an alt-splicing site? > > Look forward to your reply. > > Keith > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Dr J Keith Vass > Bioinformatics Unit, > Cancer Research UK Beatson Institute > Garscube Estate > Bearsden > Glasgow G61 1BD > > eMail k.vass@beatson.gla.ac.uk > FAX (44) (0)141 942 6521 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

On Wed, Aug 27, 2003 at 03:18:34PM +0100, Keith Vass wrote: > Hi all > > I have used affy to get perfect-match probe data for a number of affy > HG-U133a chips and I get the probes as follows 210298_x_at1, 210298_x_at2 > etc > > How do I find out what the mapping is to the oligodata that Affymetrix > give for their probes as I want to know the position the oligos bind to in > the sequence as this is a gene with an alt-splicing site? > > Look forward to your reply. > > Keith > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Dr J Keith Vass > Bioinformatics Unit, > Cancer Research UK Beatson Institute > Garscube Estate > Bearsden > Glasgow G61 1BD > > eMail k.vass@beatson.gla.ac.uk > FAX (44) (0)141 942 6521 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Hi Keith, I did this kind of job with Affymetrix chips very recently (and I have a something submitted about the study). There is a documentation on its way where I detail all the steps and intermediate results (no yet complete, hence not yet fully public). In the meanwhile, I'd be happy to try to help you off-list if you wish. As a first step, you may want to get the packages Biobase (devel-version), matchprobes (in the 'devel' section) and splicegear (also in the 'devel' section - for a reason I still did not elucidate it does not build for Windows there, if you need the MSWindows version try http://www.cbs.dtu.dk/laurent/download/splicegear/ ). Best, Laurent -- -------------------------------------------------------------- currently unspecified location -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent