Question

Invalid result from biomaRt

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 9 hours ago

United States

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"
)

biomaRt • 541 views

ADD COMMENT • link 5.3 years ago James W. MacDonald 65k

score 0 · Answer 1 · 2019-01-07

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Mike Smith ★ 6.5k

@mike-smith

Last seen 4 hours ago

EMBL Heidelberg

The main Ensembl site seems to be very slow for me at the moment. I can't even get the useMart() step to work reliably. Do you get the same behaviour if you try a mirror? e.g.

mart <- useEnsembl("ensembl","sscrofa_gene_ensembl", mirror = 'uswest')

ADD COMMENT • link 5.3 years ago Mike Smith ★ 6.5k

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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 from useMart, but didn't know you made an alternate function.

ADD REPLY • link 5.3 years ago James W. MacDonald 65k

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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.

ADD REPLY • link 5.3 years ago Mike Smith ★ 6.5k