Well, yes and no. The useProbeInfo vignette in the annotate package shows how to find locations in gene sequences. To switch to chromosomes is not hard, you would need to obtain and read in the chromosomal sequence and do the matching (worry about both strands). the packages: matchprobes and to a greater extent Biostrings have appropriate sequence matching tools - please feel free to contribute more polished versions, should you develop them. In my experience it is very fast [you could also just use regular string matching, but be careful as some of those will only return the first match, by default, and you will want all matches]. Oosting, J. (PATH) wrote: > For a single probeset it is easiest to go to the netaffx site and look > at the Probe Info: Probe Interrogation Position > > If you want to check a lot of probesets, you could have a look at the > psl document available for your chiptype. I'm not aware of any > bioconductor package that uses this filetype. > > I'm in the process of doing something with probe locations myself, and > am planning to use the last approach. > > Jan Oosting > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of pingzhao Hu > Sent: dinsdag 24 januari 2006 5:20 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] Chromosome location for probes > > Hi, > > For a probeset, say 1010_at, its chromosome location (chr22) is > 49004598-49011189. > Assume the probeset has 16 PM probes, how can I get these > probes' chromosome locations? > > Can any functions in bioconductor packages do this job ? > > Thanks, > > Pingzhao > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

Hi, You also have a java app available from the NetAffx web site which allow you to see the chromosomal location of the probe in your probeset in an interactive interface (zoom ect...). the app is call: Integrated Genome Browser and is free. best, David Ruau On Jan 25, 2006, at 9:46, Oosting, J. (PATH) wrote: > For a single probeset it is easiest to go to the netaffx site and look > at the Probe Info: Probe Interrogation Position > > If you want to check a lot of probesets, you could have a look at the > psl document available for your chiptype. I'm not aware of any > bioconductor package that uses this filetype. > > I'm in the process of doing something with probe locations myself, and > am planning to use the last approach. > > Jan Oosting > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of pingzhao > Hu > Sent: dinsdag 24 januari 2006 5:20 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] Chromosome location for probes > > Hi, > > For a probeset, say 1010_at, its chromosome location (chr22) is > 49004598-49011189. > Assume the probeset has 16 PM probes, how can I get these > probes' chromosome locations? > > Can any functions in bioconductor packages do this job ? > > Thanks, > > Pingzhao > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >