Probe Coordinates for the Affymetrix U133 2.0 plus array in the UCSC genome browser

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jason0701 ▴ 190

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Hi list, I wonder whether anyone could point me a resource (e.g. bed files) so that I can display the mapping of each probe (not probesets) in the genome browser. There was a track in UCSC browser a while ago, but couldn't be found anymore. Sorry for the question not being directly related to bioconductor. Thanks, Jason

probe probe • 1.1k views

ADD COMMENT • link updated 13.1 years ago by James W. MacDonald 67k • written 13.1 years ago by jason0701 ▴ 190

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James W. MacDonald 67k

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Hi Jason, On 10/24/2011 10:07 AM, Jason Lu wrote: > Hi list, > > I wonder whether anyone could point me a resource (e.g. bed files) so > that I can display the mapping of each probe (not probesets) in the > genome browser. There was a track in UCSC browser a while ago, but > couldn't be found anymore. It's still there, under the expression heading. Best, Jim > > Sorry for the question not being directly related to bioconductor. > > Thanks, > Jason > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

ADD COMMENT • link 13.1 years ago James W. MacDonald 67k

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Hi Jame, >From what I see, it only displays the mapping of the consensus/exampler sequences, not the mapping of each probes (which seems to be obvious to have). Thanks. Jason On Mon, Oct 24, 2011 at 10:44 AM, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > Hi Jason, > > On 10/24/2011 10:07 AM, Jason Lu wrote: >> >> Hi list, >> >> I wonder whether anyone could point me a resource (e.g. bed files) so >> that I can display the mapping of each probe (not probesets) in the >> genome browser. There was a track in UCSC browser a while ago, but >> couldn't be found anymore. > > It's still there, under the expression heading. > > Best, > > Jim > > >> >> Sorry for the question not being directly related to bioconductor. >> >> Thanks, >> Jason >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues >

ADD REPLY • link 13.1 years ago jason0701 ▴ 190

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Hi Jason, On 10/24/2011 10:57 AM, Jason Lu wrote: > Hi Jame, > > From what I see, it only displays the mapping of the > consensus/exampler sequences, not the mapping of each probes (which > seems to be obvious to have). I see your point. A Bioconductor-centric solution to this problem would be to use matchPDict() from Biostrings along with the BSgenomes and the BSgenome.Hsapiens.UCSC.hg19 packages (and obviously the hgu133plus2probe package). The help page for matchPDict() should get you about 80% of the way there. If you unlist() the output from matchPDict(), you get an IRanges object that you can output in bed format using export.bed() from rtracklayer. Best, Jim > > Thanks. > > Jason > > > On Mon, Oct 24, 2011 at 10:44 AM, James W. MacDonald > <jmacdon at="" med.umich.edu=""> wrote: >> Hi Jason, >> >> On 10/24/2011 10:07 AM, Jason Lu wrote: >>> Hi list, >>> >>> I wonder whether anyone could point me a resource (e.g. bed files) so >>> that I can display the mapping of each probe (not probesets) in the >>> genome browser. There was a track in UCSC browser a while ago, but >>> couldn't be found anymore. >> It's still there, under the expression heading. >> >> Best, >> >> Jim >> >> >>> Sorry for the question not being directly related to bioconductor. >>> >>> Thanks, >>> Jason >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not be >> used for urgent or sensitive issues >> -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

ADD REPLY • link 13.1 years ago James W. MacDonald 67k

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