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?

Thanks again,
Shirley

On Thu, Jul 19, 2012 at 9:11 AM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Hi Shirley,
>
> Does this have what you want?
>
> http://bioconductor.org/**packages/2.10/data/annotation/**html/**
> HuExExonProbesetLocationHg19.**html<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
>>
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
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> Seattle WA 98105-6099
>
>

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