BioMart webservice returned an invalid result
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mcall ▴ 20
@mcall-11507
Last seen 3.0 years ago

Hi!

Since yesterday I'm trying to annotate based on Ensembl ids, however, in some cases it works, but the majority of the times that I try, I receive the following error:

Batch submitting query [=================================================================================>------] 94% eta: 49sError in getBM(attributes = columns, filters = keytype, values = keys, : 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

What else should I send?

Many thanks,

Maria

software error annotation BioMart • 285 views
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You should also send the code that preceded that call, and better yet a self-contained example that anybody can run to replicate the error. In addition, the output from running sessionInfo.

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Mike Smith ★ 5.9k
@mike-smith
Last seen 8 hours ago
EMBL Heidelberg

It might be that the main Ensembl site is being a bit slow today. You can try querying one of the mirror sites e.g.

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

Values for the mirror argument are: useast, uswest, asia. You'll need to modified the dataset argument if you're not accessing human genes.

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