[BioC] Probe Coordinates for the Affymetrix U133 2.0 plus array in the UCSC genome browser

[James W. MacDonald]

Hi Jason,

On 10/24/2011 10:57 AM, Jason Lu wrote:
> Hi Jame,
>
>  From what I see, it only displays the mapping of the
> consensus/exampler sequences, not the mapping of each probes (which
> seems to be obvious to have).

I see your point. A Bioconductor-centric solution to this problem would 
be to use matchPDict() from Biostrings along with the BSgenomes and the 
BSgenome.Hsapiens.UCSC.hg19 packages (and obviously the hgu133plus2probe 
package).

The help page for matchPDict() should get you about 80% of the way 
there. If you unlist() the output from matchPDict(), you get an IRanges 
object that you can output in bed format using export.bed() from 
rtracklayer.

Best,

Jim


>
> Thanks.
>
> Jason
>
>
> On Mon, Oct 24, 2011 at 10:44 AM, James W. MacDonald
> <jmacdon at med.umich.edu>  wrote:
>> Hi Jason,
>>
>> On 10/24/2011 10:07 AM, Jason Lu wrote:
>>> Hi list,
>>>
>>> I wonder whether anyone could point me a resource (e.g. bed files) so
>>> that I can display the mapping of each probe (not probesets) in the
>>> genome browser. There was a track in UCSC browser a while ago, but
>>> couldn't be found anymore.
>> It's still there, under the expression heading.
>>
>> Best,
>>
>> Jim
>>
>>
>>> Sorry for the question not being directly related to bioconductor.
>>>
>>> Thanks,
>>> Jason
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> Douglas Lab
>> University of Michigan
>> Department of Human Genetics
>> 5912 Buhl
>> 1241 E. Catherine St.
>> Ann Arbor MI 48109-5618
>> 734-615-7826
>>
>> **********************************************************
>> Electronic Mail is not secure, may not be read every day, and should not be
>> used for urgent or sensitive issues
>>

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826

**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues