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 >