Error in getBM(attributes)
1
0
Entering edit mode
ross.kedl • 0
@rosskedl-22870
Last seen 4.6 years ago

in submitting a getBM(attributes) request to BioMart, i received this error message:

"Error in getBM(attributes = c("ensembltranscriptidversion", "ensemblgene_id", : 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."

it has happened twice now so am reporting it. i in the same document, this worked fine the day previous. any assistance is greatly appreciated

software error • 316 views
ADD COMMENT
0
Entering edit mode
Mike Smith ★ 6.5k
@mike-smith
Last seen 8 hours ago
EMBL Heidelberg

This usually indicates some instability with the main Ensembl webserver. You can try querying one of the mirrors e.g.

mart <- useEnsembl(biomart = "ensembl", 
                   dataset = "dmelanogaster_gene_ensembl", 
                   mirror = "useast")

Values for the mirror argument are: useast, uswest, asia

I've updated the developmental version of biomaRt to try and detect this and do the redirection automatically in the future.

ADD COMMENT

Login before adding your answer.

Traffic: 592 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6