getBM biomart ensembl Error report
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nina.hahn • 0
@ninahahn-23355
Last seen 17 months ago

Dear all,

I am not very familiar with R and get error massages like this:

"Batch submitting query [==================================>------------------] 67% eta: 3sError in getBM(filters = "ensemblgeneid", attributes = c("ensemblgeneid", : 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"

They are all the same but differ in progress [%] and time [s]. A few days before everything was working but today I get this error but did not changed the script, the raw data or updated anything.

What might be a problem?

Best, Nina

biomaRt ensembl • 574 views
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Mike Smith ★ 5.1k
@mike-smith
Last seen 1 hour ago
EMBL Heidelberg / de.NBI

If you didn't change anything and the code worked previously then it's almost certainly a problem with the Ensembl server. You can try using a mirror site e.g.

You could try querying one of the mirror sites, to see if it's more responsive.

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

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

When you get the "batch submitting" message biomaRt should also cache blocks of interim results. It won't show them too you, but if you run the exact query again the progress bar will always get further than it did last time until it reaches the end. This was added so that you should always be able to eventually complete long queries, even if the server is being unstable. If that's not what it's doing in this case please let me know.

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That answer is great and even comprehensive for me as a beginner.

It solved the problem and I will be able to cope with that problem in the future.

Thanks a lot!

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