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

[Hervé Pagès]

Hi Shirley, James,

On 07/19/2012 07:15 AM, James W. MacDonald wrote:
> 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'.

I think the matchAffyProbes() function in the altcdfenvs package (which
is based on matchPDict()) does that too and might be a little bit more
convenient to use.

Cheers,
H.

>
> 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
>>
>>
>>
>


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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