Hi, There was an email to this list a few days ago about a similar (I think) problem with GO queries failing. It seems appropriate here(?). Apparently the identifiers for GO stuffs has changed, see the thread that starts here: https://stat.ethz.ch/pipermail/bioconductor/2011-May/039435.html The original poster was querying with something like: attributes=c("entrezgene", "go_cellular_component_id", "go_cellular_component__dm_name_1006") And was getting errors. Apparently: """the three GO sections have been merged into one. See here for news about ensembl BioMart changes: http://www.ensembl.org/info/website/news/index.html#team-Mart These are the names of the attributes you now need to look for: <query virtualschemaname="default" formatter="TSV" header="0" uniquerows="0" count="" datasetconfigversion="0.6"> <dataset name="hsapiens_gene_ensembl" interface="default"> <attribute name="go_id"/> <attribute name="name_1006"/> <attribute name="definition_1006"/> <attribute name="go_linkage_type"/> <attribute name="namespace_1003"/> </dataset> </query> These attribute names correspond to: GO Term Accession GO Term Name GO Term Definition GO Term Evidence Code GO domain """" Hope that helps, -steve On Tue, May 17, 2011 at 2:44 AM, Wolfgang Huber <whuber at="" embl.de=""> wrote: > Konika > > thanks. Your 'sample code' is incomplete. How did you define the object > 'ensembl'? > > ? ? ? ?Best wishes > ? ? ? ?Wolfgang > > > chawla scripsit 05/15/2011 11:53 PM: >> >> Hi >> I have used BiomaRt to retrieve GO terms for affymetrix probe Ids using >> mart ensembl. >> But suddenly all the GO terms attributes have vanished from the list of >> attributes. >> I used the sample code to test. >> >> ?> affyids = c("202763_at", "209310_s_at", "207500_at") >> ?> getBM(attributes = c("affy_hg_u133_plus_2", >> "go_biological_process_id", "chromosome_name", "start_position", >> + "end_position", "band"), filters = "affy_hg_u133_plus_2", values = >> affyids, mart = ensembl) >> Error in getBM(attributes = c("affy_hg_u133_plus_2", >> "go_biological_process_id", : >> Invalid attribute(s): go_biological_process_id >> Please use the function 'listAttributes' to get valid attribute names >> >> I am thus unable to reproduce previous results. >> Have no idea how this could happen, If anyone can help it will be great. >> Thanks >> Konika >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact