I succeeded in retrieving data from dataset athaliana_gene_ensembl (see the following example). But I do not know how to retrieve the GO annotations using function getBM. I mean, I do not know which attributes return the GO information for item in such a dataset. Any halp is more than welcome. Thank you in advance, Maura > gramene<-useMart('ENSEMBL_MART_ENSEMBL',dataset="athaliana_gene_ense mbl") Checking attributes ... ok Checking filters ... ok # EXAMPLE > go<-getBM(attributes="ensembl_gene_id",values="245042_at",filters="a ffy_ath1", mart=gramene) > go ensembl_gene_id 1 AT2G26540-TAIR-G .html?pmk=footer> [[alternative HTML version deleted]]

Hi Maura, I am sorry that your question is a little opaque to me so I will guess from you code that you are trying to get GO annotations for probesets? In addition to biomaRt, you could use one of the affy chip annotation packages that we have here (depending which platform you needed). http://www.bioconductor.org/packages/devel/data/annotation/html/ag.db. html http://www.bioconductor.org/packages/devel/data/annotation/html/ath112 1501.db.html If it was data about the internal structure of GO that you wanted, you could use GO.db. http://www.bioconductor.org/packages/devel/data/annotation/html/GO.db. html Hope this answers your questions, Marc mauede at alice.it wrote: > I succeeded in retrieving data from dataset athaliana_gene_ensembl (see the following example). > > But I do not know how to retrieve the GO annotations using function getBM. > > I mean, I do not know which attributes return the GO information for item in such a dataset. > > Any halp is more than welcome. > > Thank you in advance, > > Maura > > >> gramene<-useMart('ENSEMBL_MART_ENSEMBL',dataset="athaliana_gene_ens embl") >> > Checking attributes ... ok > Checking filters ... ok > > # EXAMPLE > >> go<-getBM(attributes="ensembl_gene_id",values="245042_at",filters=" affy_ath1", mart=gramene) >> go >> > ensembl_gene_id > 1 AT2G26540-TAIR-G > > > > > .html?pmk=footer> > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > >