[BioC] Chromosome location for probes

Robert Gentleman rgentlem at fhcrc.org
Wed Jan 25 16:21:56 CET 2006

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
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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
rgentlem at fhcrc.org

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