[BioC] obtain the chromosome position/coordinates for probes on Affymetrix Human Exon 1.0 array

[James W. MacDonald]

Hi Shirley,

On 7/19/2012 10:02 AM, shirley zhang wrote:
> Thanks Jim for your information.
>
> The package you pointed out only provides the Exon-level probeset 
> chromosome location. What I want is probe-level chromosome location. 
> For each 25bp probe, Affymetrix provides its sequence, and positionX 
> and positionY on the Chip, but not the position on Human reference genome.
>
> Do you have any other suggestions? Does package GenomeFeatures have 
> this functionality?

No, that package is designed to deal with already aligned data (for 
which you would already have the data you desire).

I would recommend using Biostrings and the requisite BSgenome package. 
Aligning fixed width sequences with no indels or mismatches is much 
simpler than the typical alignment problem, for which matchPDict() is 
ideally suited.

Please see

http://bioconductor.org/packages/2.10/bioc/vignettes/BSgenome/inst/doc/GenomeSearching.pdf

particularly section 8, 'Finding all the patterns of a constant width 
dictionary in an entire genome'.

Best,

Jim


>
> Thanks again,
> Shirley
>
> On Thu, Jul 19, 2012 at 9:11 AM, James W. MacDonald <jmacdon at uw.edu 
> <mailto:jmacdon at uw.edu>> wrote:
>
>     Hi Shirley,
>
>     Does this have what you want?
>
>     http://bioconductor.org/packages/2.10/data/annotation/html/HuExExonProbesetLocationHg19.html
>
>     Best,
>
>     Jim
>
>
>
>
>     On 7/18/2012 10:38 PM, shirley zhang wrote:
>
>         Dear list,
>
>         I am trying to retrieve the chromosome position/coordinates
>         for each 25bp
>         probe on Affymetrix Human Exon 1.0 array. I checked
>         Affymetrix's website
>         and found that Affymetrix only provides the genome position
>         for each
>         probeset/exon, and also provides the sequence information for
>         each probe.
>
>         I understand that I could first download the probe sequence from
>         Affymetrix, and then BLAT them against Human Reference Genome
>         to get the
>         position. However, before I try BLAT, I am wondering whether
>         anyone has
>         already done the alignment using BLAT or other tools, and
>         would like to
>         share the probe position for each probe on Exon array. If the
>         position is
>         based on hg19/build 37, it would be more helpful.
>
>         Thanks in advance!
>
>         Shirley
>
>                 [[alternative HTML version deleted]]
>
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>
>     -- 
>     James W. MacDonald, M.S.
>     Biostatistician
>     University of Washington
>     Environmental and Occupational Health Sciences
>     4225 Roosevelt Way NE, # 100
>     Seattle WA 98105-6099
>
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099