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.