Re: [Celsius-users] SN identifiers to GEO accession?

[louis f. <lou...@gm...>]

Mr. Hassane,

Yes, there is a way to find the GEO GSM corresponding to a SNID:
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Using the URL:
http://celsius.genomics.ctrl.ucla.edu/service/search/cel_accession?q=SN:1000119
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Yeilds:
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Results for "SN:1000119":

    * Query: SN:1000119
          o Target: SN:1000119
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Clicking on SN:1000119 yeilds:
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CEL SN:1000119 (MG_U74Av2)
Download:
as BED: RMA GCRMA
as EGR: RMA GCRMA



Tag with:       <ENTER> to save.
Annotate with:  <ENTER> to save.
suggestions

Web annotations associated with SN:1000119
Ontology        Term    Value   Weight
Web tags associated with SN:1000119
Username        Tags

Blessed annotations associated with SN:1000119
Ontology        Term    Partition

Accessions associated with SN:1000119
Database        Accession
GEO     GSE775
GEO     GSM12345
SN      1000119
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On 10/23/07, Hassane, Duane <Dua...@ur...> wrote:
>
>  Hi,
>
> I read with great enthusiasm your recent report in Genome Biology
> regarding the Celsius project.  It's obviously of great value to take
> primary microarray data and apply consistent normalization to make data more
> comparable, congratulations!
>
> I have been attempting to utilize the RMA normalized data for the
> U133-based platforms and realize that the R interface provides a means of
> using GEO accessions to map to Celsius identifiers.  Looking through the R
> scripts of the celsius package, I can see how to, e.g., download a
> tab-delimited text file containing the complete annotation for a particular
> platform using a tool like wget.  However, I would also like to be able to
> take a list of "SN" identifiers and map them to GEO GSM accession numbers
> (or otherwise identifiers and descriptions in the original repository from
> which the CEL was first derived).
>
> Is there a convenient way of doing this?  I have not noted such
> information in the downloaded annotations so far.
>
> I apologize in advance if I am missing something fairly obvious.
>
> Again, great and important work.
>
> Thanks,
>
> Duane Hassane
>
>
>
>
>
> THE CONTENTS OF THIS MESSAGE ARE CONFIDENTIAL
> _________________________________________________
> Duane C. Hassane, Ph.D.
> Center for Pediatric Biomedical Research
> University of Rochester Medical Center
> 601 Elmwood Avenue, Box 703
> MRBX Room 1-11115
> Rochester, New York 14642
> Tel: 585-275-9680
> Fax: 585-276-0232
> E-mail: dua...@ur...
>
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>


-- 
Lou Fridkis
UCLA Geffen School of Medicine
Department of Human Genetics
Nelson Lab
695 Charles E Young Drive S.
Los Angeles, CA 90095 USA
310-825-7920