Question: Any changes in Biomart regarding GO terms? Script crashing today
8.5 years ago by
J.delasHeras@ed.ac.uk • 1.9k
J.delasHeras@ed.ac.uk • 1.9k wrote:
I am unable to run a script I have been using quite happily in the past, so I suspect a change in the "outside world", but I can't find any news about it. It appears that the usual attributes for GO terms and IDs (CC, BP and MF) are not available. (?) If you try this quick example: library(biomaRt) ensembl=useMart("ensembl") dataset="hsapiens_gene_ensembl" ensembl=useDataset(dataset, mart=ensembl) attributes=c("entrezgene", "go_cellular_component_id", "go_cellular_component__dm_name_1006") getBM(attributes=attributes, filters="entrezgene", values=1, mart=ensembl) It fails with the error: Error in getBM(attributes = attributes, filters = "entrezgene", values = 1, : Invalid attribute(s): go_cellular_component_id, go_cellular_component__dm_name_1006 Please use the function 'listAttributes' to get valid attribute names and if you list the attributes... listAttributes(ensembl) you can see they're indeed not listed... am I right thinking this has nothing to do with the biomaRt R side of things? Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6507090 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
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