Affymetrix annotation package

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Hans-Ulrich Klein ▴ 330

@hans-ulrich-klein-1945

Last seen 7 months ago

United States

Dear list, I wonder about the annotation of some probesets on Affymetrix chips. E.g.: > library("hgu95av2") > get("1726_at", env=hgu95av2ACCNUM) [1] "HG919-HT919" Is "HG919-HT919" really an accession number? I do not get any hits at NCBI's GenBank. NetAffx gives the same identifier for that probeset, but in a field called "Representative Public ID". There are some more probesets with "HGXXX-HTXXX" as ACCNUM on the hgu95av2 chip. Where can get more information about this identifiers? Thanks, Hans-Ulrich

Annotation Annotation • 1.4k views

ADD COMMENT • link updated 16.7 years ago by John Zhang ★ 2.9k • written 16.7 years ago by Hans-Ulrich Klein ▴ 330

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 14 hours ago

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Hi Hans, Did you try Google? I find the first item on that list to be pretty informative. Best, Jim Hans-Ulrich Klein wrote: > Dear list, > > I wonder about the annotation of some probesets on Affymetrix chips. E.g.: > >> library("hgu95av2") >> get("1726_at", env=hgu95av2ACCNUM) > [1] "HG919-HT919" > > Is "HG919-HT919" really an accession number? I do not get any hits at NCBI's GenBank. NetAffx gives the same identifier for that probeset, but in a field called "Representative Public ID". > There are some more probesets with "HGXXX-HTXXX" as ACCNUM on the hgu95av2 chip. Where can get more information about this identifiers? > > Thanks, > Hans-Ulrich > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > 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 Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

ADD COMMENT • link 16.7 years ago James W. MacDonald 65k

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I've noticed some discrepancies with annotations, also. At least for human, GeneCards has links from affy_id to other useful data. It is somewhat manual, though. Example: http://rcdev.umassmed.edu/cgi- bin/genecards/carddisp.pl?gene=POLE&search =1726_at&suff=txt -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of James W. MacDonald Sent: Tuesday, July 31, 2007 9:27 AM To: Hans-Ulrich Klein Cc: Bioconductor list Subject: Re: [BioC] Affymetrix annotation package Hi Hans, Did you try Google? I find the first item on that list to be pretty informative. Best, Jim Hans-Ulrich Klein wrote: > Dear list, > > I wonder about the annotation of some probesets on Affymetrix chips. E.g.: > >> library("hgu95av2") >> get("1726_at", env=hgu95av2ACCNUM) > [1] "HG919-HT919" > > Is "HG919-HT919" really an accession number? I do not get any hits at NCBI's GenBank. NetAffx gives the same identifier for that probeset, but in a field called "Representative Public ID". > There are some more probesets with "HGXXX-HTXXX" as ACCNUM on the hgu95av2 chip. Where can get more information about this identifiers? > > Thanks, > Hans-Ulrich > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > 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 Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD REPLY • link 16.7 years ago David Lapointe ▴ 190

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Hi, You might also want to have a look at ADAPT for standard 3' arrays: http://bioinf.picr.man.ac.uk/adapt, and X:Map: http://xmap.picr.man.ac.uk for exon arrays. Crispin > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > Lapointe, David > Sent: 31 July 2007 15:17 > Cc: Bioconductor list > Subject: Re: [BioC] Affymetrix annotation package > > I've noticed some discrepancies with annotations, also. At > least for human, GeneCards has links from affy_id to other > useful data. It is somewhat manual, though. > > Example: > http://rcdev.umassmed.edu/cgi-bin/genecards/carddisp.pl?gene=P > OLE&search > =1726_at&suff=txt > > > <snip> -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}

ADD REPLY • link 16.7 years ago Crispin Miller ★ 1.1k

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John Zhang ★ 2.9k

@john-zhang-6

Last seen 9.6 years ago

>> >> Is "HG919-HT919" really an accession number? I do not get any hits at NCBI's GenBank. NetAffx gives the same identifier for that probeset, but in a field called "Representative Public ID". >> There are some more probesets with "HGXXX-HTXXX" as ACCNUM on the hgu95av2 chip. Where can get more information about this identifiers? The Public IDs Affymetrix provides may be a mixture of GenBank and other IDs. Since most of the IDs on earlier arrays are GenBank IDs, BioC annoation package names the environment "ACCNUM", although they are not all GenBank IDs. In fact, some of the IDs (not sure if this applies to the 95av2 chip) are TIGR IDs. I used Google to figure out the identity of the non-GeneBank ids. >> >> Thanks, >> Hans-Ulrich >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> 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 >Affymetrix and cDNA Microarray Core >University of Michigan Cancer Center >1500 E. Medical Center Drive >7410 CCGC >Ann Arbor MI 48109 >734-647-5623 > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

ADD COMMENT • link 16.7 years ago John Zhang ★ 2.9k

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