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

[James W. MacDonald]

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