Entering edit mode
When querying for GO IDs for pig, I get the following error, which isn't completely reproducible:
> mart <- useMart("ensembl","sscrofa_gene_ensembl")
> tmp <- getBM(c("ensembl_gene_id","go_id"), "ensembl_gene_id", zzz, mart)
> tmp <- getBM(c("ensembl_gene_id","go_id"), "ensembl_gene_id", zzz, mart)
Error in getBM(c("ensembl_gene_id", "go_id"), "ensembl_gene_id", zzz, :
The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1.
Please report this on the support site at http://support.bioconductor.org
> tmp <- getBM(c("ensembl_gene_id","go_id"), "ensembl_gene_id", zzz, mart)
>
> dput(zzz)
c("ENSSSCG00000017411", "ENSSSCG00000017414", "ENSSSCG00000017415",
"ENSSSCG00000017416", "ENSSSCG00000017417", "ENSSSCG00000017418",
"ENSSSCG00000017419", "ENSSSCG00000017420", "ENSSSCG00000017421",
"ENSSSCG00000017422", "ENSSSCG00000017427", "ENSSSCG00000017428",
"ENSSSCG00000017429", "ENSSSCG00000017430", "ENSSSCG00000017433",
"ENSSSCG00000017437", "ENSSSCG00000017438", "ENSSSCG00000017439",
"ENSSSCG00000017441", "ENSSSCG00000017444", "ENSSSCG00000017445",
"ENSSSCG00000017446", "ENSSSCG00000017448", "ENSSSCG00000017450",
"ENSSSCG00000017451", "ENSSSCG00000017458", "ENSSSCG00000017459",
"ENSSSCG00000017461", "ENSSSCG00000017462", "ENSSSCG00000017463",
"ENSSSCG00000017464", "ENSSSCG00000017465", "ENSSSCG00000017466",
"ENSSSCG00000017470", "ENSSSCG00000017471", "ENSSSCG00000017472",
"ENSSSCG00000017473", "ENSSSCG00000017474", "ENSSSCG00000017475",
"ENSSSCG00000017476", "ENSSSCG00000017477", "ENSSSCG00000017478",
"ENSSSCG00000017479", "ENSSSCG00000017488", "ENSSSCG00000017489",
"ENSSSCG00000017490", "ENSSSCG00000017492", "ENSSSCG00000017493"
)
That seems to be the problem. Thanks for the pointer to
useEnsembl. I didn't know that function existed; I knew you removed the redirect argument fromuseMart, but didn't know you made an alternate function.That function has actually been there for years, but was very rarely used in examples or documentation. Since 99% of the biomaRt questions are related to Ensembl, I thought I would start making it more visible. I find the mirror argument easier to remember than typing in the alternative URLs, hopefully others do to.