Howto Get GO/Gene-names of GEO-Soft Probe-names
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@gundala-viswanath-2872
Last seen 9.6 years ago
Dear all, I have the following probe names selected from a dataset (GDS592), taken from GEO (SOFT format). gnf1m29878_a_at gnf1m13556_at gnf1m09610_a_at gnf1m11352_a_at gnf1m26036_at ...more... And I want to get the GO term and Official Gene Name from these probe names. Is there a way to do it? I tried these two Bioconductor commands but fail. > library("hgu95av2.db") > hgu95av2SYMBOL[["gnf1m2978_a_at"]] NULL > hgu95av2GO[["gnf1m2978_a_at"]] NULL Please advice. - Gundala Viswanath Jakarta - Indonesia
GO probe GO probe • 996 views
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@cei-abreu-goodger-4433
Last seen 9.1 years ago
Mexico
Hi Gundala, Those probes are from the GNF mouse custom affymetrix array, and are as such not directly supported in bioconductor. But, you can easily construct an annotation package for this chip. Check out the vignette for SQLForge that comes with: library(AnnotationDbi) You will need to prepare a text file with 2 columns, in the first the probe id and in the second a commonly used gene/transcript identifier such as Entrez, GeneBank, RefSeq... you can get this information directly from the NCBI or from the GNF website. Cheers, Cei On Sun, 27 Jul 2008, Gundala Viswanath wrote: > Dear all, > > I have the following probe names selected from a dataset (GDS592), > taken from GEO (SOFT format). > > gnf1m29878_a_at > gnf1m13556_at > gnf1m09610_a_at > gnf1m11352_a_at > gnf1m26036_at > ...more... > > And I want to get the GO term and Official Gene Name from these > probe names. > > Is there a way to do it? > > I tried these two Bioconductor commands but fail. > >> library("hgu95av2.db") >> hgu95av2SYMBOL[["gnf1m2978_a_at"]] > NULL >> hgu95av2GO[["gnf1m2978_a_at"]] > NULL > > Please advice. > > - Gundala Viswanath > Jakarta - Indonesia > > _______________________________________________ > 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 > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
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On Sun, Jul 27, 2008 at 7:05 AM, Cei Abreu-Goodger <cei at="" sanger.ac.uk=""> wrote: > > Hi Gundala, > > Those probes are from the GNF mouse custom affymetrix array, and are as such > not directly supported in bioconductor. But, you can easily construct an > annotation package for this chip. Check out the vignette for SQLForge that > comes with: > library(AnnotationDbi) > > You will need to prepare a text file with 2 columns, in the first the probe > id and in the second a commonly used gene/transcript identifier such as > Entrez, GeneBank, RefSeq... you can get this information directly from the > NCBI or from the GNF website. Just to add a bit here, the development branch of GEOquery includes a flag to get the annotation GPL SOFT file for a GDS. The annotation GPLs contain GO information for the probes, generally. Sean > On Sun, 27 Jul 2008, Gundala Viswanath wrote: > >> Dear all, >> >> I have the following probe names selected from a dataset (GDS592), >> taken from GEO (SOFT format). >> >> gnf1m29878_a_at >> gnf1m13556_at >> gnf1m09610_a_at >> gnf1m11352_a_at >> gnf1m26036_at >> ...more... >> >> And I want to get the GO term and Official Gene Name from these >> probe names. >> >> Is there a way to do it? >> >> I tried these two Bioconductor commands but fail. >> >>> library("hgu95av2.db") >>> hgu95av2SYMBOL[["gnf1m2978_a_at"]] >> >> NULL >>> >>> hgu95av2GO[["gnf1m2978_a_at"]] >> >> NULL >> >> Please advice. >> >> - Gundala Viswanath >> Jakarta - Indonesia >> >> _______________________________________________ >> 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 >> > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research Limited, > a charity registered in England with number 1021457 and a company registered > in England with number 2742969, whose registered office is 215 Euston Road, > London, NW1 2BE. > > _______________________________________________ > 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 >
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