Question

Error in getBM

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erockkirk ▴ 20

@erockkirk-21353

Last seen 5.4 years ago

There seems to be an error with the getBM function in biomaRt. The below code was working 3 days ago and now returns an error message. Any help would be appreciated. I'm working in R (version 3.6.0).

mart <- biomaRt::useMart(biomart = "ensembl", + dataset = "hsapiensgeneensembl", + host = 'http://www.ensembl.org')

ttg <- biomaRt::getBM( + attributes = c('mirbaseaccession', + 'mirbaseid', + 'mirbasetransname'), + mart = mart)

Error in biomaRt::getBM(attributes = c("mirbaseaccession", "mirbaseid", : The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1.

software error • 1.7k views

ADD COMMENT • link updated 5.4 years ago by YinCY ▴ 20 • written 5.4 years ago by erockkirk ▴ 20

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The same problem happens to me right now, and it happened to me a couple of weeks ago too. . it's related to the web server of Ensembl, it's not working well. Hope there is a solution... Maybe it's a matter of time.

ADD REPLY • link 5.4 years ago rgeysels • 0

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one solution I found was to use a different host, or alternate to whichever is working. host = 'http://useast.ensembl.org'

ADD REPLY • link 5.4 years ago erockkirk ▴ 20

score 2 · Answer 1 · 2019-07-17

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YinCY ▴ 20

@yincy-17934

Last seen 5.4 years ago

HangZhou, zhejaing

Try use useEnsembl() function instead of useMart() which can choose different mirror, that you can choose the one that closest to you. useEnsembl(mirror = c("eastusa", "westusa", "asia"))

ADD COMMENT • link 5.4 years ago YinCY ▴ 20

score 0 · Answer 2 · 2019-07-15

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Puks ▴ 10

@puks-12113

Last seen 4.5 years ago

Estonia

A previous post on this might be helpful for you: https://support.bioconductor.org/p/121331/

ADD COMMENT • link 5.4 years ago Puks ▴ 10