Although it is not a BioConductor solution, you should check out the Splice
Center website at the NIH for a nice view of probe locations across
isoforms.
On Jul 2, 2012 10:54 AM, "Steve Lianoglou" <mailinglist.honeypot@gmail.com>
wrote:

> Hi Jiayi,
>
> Side note: please CC the bioconductor list when replying to emails so
> they can stay online -- you'll get better help (more eyeballs on your
> problem), and the list can be used as a resource to others.
>
> I guess this might be a pain using the "guest posting" stuff -- but
> subscribing to the mailing list is easy, and you'll learn a lot by
> skimming the post that come through here.
>
> OK -- now to solver your problem:
>
> On Mon, Jul 2, 2012 at 11:03 AM, Jiayi Hou <houj2@vcu.edu> wrote:
> > Hey Steve,
> >
> > Sorry let me put it this way, so when a probeset hybridized to a given
> gene,
> > the gene has a chromosomal location in terms of base pair. For a given
> gene,
> > on average there may be 2-3 probesets attach to the same gene. However,
> > these 2-3 probesets carrying different sequence of base pairs, are
> expected
> > to attach to the different location oin the given gene. What I am looking
> > for is where precisly these probesets attach to the gene.
>
> Thanks, that's a bit clearer now.
>
> In the past I've done this with a little elbow grease: you can get the
> probe sequence info for the chip you're using from this package:
>
>
> http://bioconductor.org/packages/2.10/data/annotation/html/htmg430aprobe.html
>
> There's a short vignette on matching probe sequences (against each
> other, which isn't all that helpful for you, but can be a start) using
> the Biostrings package here:
>
>
> http://bioconductor.org/packages/2.10/bioc/vignettes/Biostrings/inst/doc/matchprobes.pdf
>
> You can extend the examples there by matching your probes against the
> mouse genome using the appropriate BSgenome package
> (BSgenome.Mmusculus.UCSC.mm9).
>
> Alternatively, you can follow section 4.1 of the biomaRt vignette here:
>
>
> http://bioconductor.org/packages/2.10/bioc/vignettes/biomaRt/inst/doc/biomaRt.pdf
>
> For example:
>
> R> ensembl <- useMart("ensembl",dataset="hsapiens_gene_ensembl")
> R> affyids <- c("202763_at","209310_s_at","207500_at")
> R> getBM(attributes=c('affy_hg_u133_plus_2', 'hgnc_symbol',
>                 'chromosome_name','start_position','end_position', 'band'),
>       filters = 'affy_hg_u133_plus_2', values = affyids, mart = ensembl)
>
>   affy_hg_u133_plus_2 hgnc_symbol chromosome_name start_position
> end_position  band
> 1           202763_at       CASP3               4      185548850
> 185570663 q35.1
> 2         209310_s_at       CASP4              11      104813593
> 104840163 q22.3
> 3           207500_at       CASP5              11      104864962
> 104893895 q22.3
>
> You'll have to change the "mart/dataset" you are using, as well as the
> chip id's, but you should get the idea.
>
> HTH,
> -steve
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

