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antoineclem1207
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@antoineclem1207-23187
Last seen 4.1 years ago
Hi,
I made getBM function to retrieve Go accession terms and numbers for a specific gene (Auts2) on ratus norvegicus genome. I found 4 accession numbers with biomaRt but when I made the same research on GO website, I found 21 accession numbers. I would like obtain all accession numbers with biomaRt. There are no error in the commands.
Thank's for for upcoming answers !
Can you update your post to include the biomaRt code you're running, and maybe also link to the page on the GO website you're using? It's very hard to comment on any differences you may be seeing without a bit more detail on what you are comparing.
Of course, R script:
library(biomaRt)
ensemblrat <- useMart ("ensembl", dataset = "rnorvegicusgeneensembl")
auts2<-getBM(attributes=c('ensemblgeneid',"entrezgeneid","chromosomename","goid","externalgenename","definition1006","name1006"), filters = ("externalgene_name"), values = ("Auts2"), mart = (ensemblrat))
GO link : http://amigo.geneontology.org/amigo/search/annotation?q=AUTS2 You need to add filter " taxonsubsetclosure_label: Rattus norvegicus", it's not keep with the link.
To complete, I obtained the same number of GO terms between biomaRt and GO website with the Human genome ...