Thank you, Marc! Best, Allen On Thu, Jul 10, 2008 at 11:23 AM, Marc Carlson <mcarlson@fhcrc.org> wrote: > Hi Allen, > > In that case you can just use the RefSeq IDs to make a custom package for > your platform of choice using the SQLForge code inside of the AnnotationDbi > package. > You can find out more here: > > http://www.bioconductor.org/packages/2.3/bioc/html/AnnotationDbi.html > > Let me know if you need more information, > > > Marc > > > > ss wrote: > >> Dear all, >> >> Hi! I have a question about using the function 'hyperGTest' in >> GOstatsHyperG. >> What if I want to find the enriched GO terms based on a set of genes which >> I >> only know gene symbol, Ensembl Gene ID, and RefSeq ID. Since the array >> is customized and I don't find the corresponding 'annotation' package in >> Bioconductor. >> >> In other words, when making the: >> >> params <- new(...,geneIds, annotation,...), would it possible for me to >> pass >> "gene symbol" >> or "Ensembl Gene ID", or "RefSeq ID" to "geneIds" and ignore "annotation" >> etc.? >> >> Thanks much! >> >> Allen >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> > > [[alternative HTML version deleted]]

Thank you, Sean! Best, Allen On Thu, Jul 10, 2008 at 11:24 AM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Thu, Jul 10, 2008 at 11:05 AM, ss <affysnp@gmail.com> wrote: > > Dear all, > > > > Hi! I have a question about using the function 'hyperGTest' in > > GOstatsHyperG. > > What if I want to find the enriched GO terms based on a set of genes > which I > > only know gene symbol, Ensembl Gene ID, and RefSeq ID. Since the array > > is customized and I don't find the corresponding 'annotation' package in > > Bioconductor. > > > > In other words, when making the: > > > > params <- new(...,geneIds, annotation,...), would it possible for me to > pass > > "gene symbol" > > or "Ensembl Gene ID", or "RefSeq ID" to "geneIds" and ignore "annotation" > > etc.? > > You can use the org.hs-type annotation package, which uses entrez gene > id as the key. So, you would need to get the Entrez Gene ID for the > genes on your chip. Given that you have RefSeq, Ensembl, and Symbol, > you can use the same annotation package to get back to Entrez Gene ID > from those other ID types. > > Sean > [[alternative HTML version deleted]]