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From: louis f. <lou...@gm...> - 2007-11-02 21:13:36
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Mr. Hassane, Yes, there is a way to find the GEO GSM corresponding to a SNID: ******************************************************************************** ******************************************************************************** Using the URL: http://celsius.genomics.ctrl.ucla.edu/service/search/cel_accession?q=SN:1000119 ******************************************************************************** Yeilds: ******************************************************************************** Results for "SN:1000119": * Query: SN:1000119 o Target: SN:1000119 ******************************************************************************** ******************************************************************************** Clicking on SN:1000119 yeilds: ******************************************************************************** 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 ******************************************************************************** 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... > > This message contains information which may be confidential and > privileged. Unless you are the addressee (or authorized to receive for the > addressee), you may not use, copy or disclose to anyone the message or any > information contained in the message (including attachments). If you have > received this message in error, please advise the sender by reply e-mail and > delete the message. > > -- 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 |