Question: The query to the BioMart webservice returned an invalid result: biomaRt expected a character string
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gravatar for lbuo
23 days ago by
lbuo0
lbuo0 wrote:

Hello, I have a problem using the function getBM in BioMart. I am using this command:

library(biomaRt) ensembl = useMart("ensembl",dataset="dreriogeneensembl") Result<- getBM(attributes=c("ensemblgeneid","externalgenename"), filters = "go", values = 'GO:0005856', mart =ensembl)

But sometimes R return me this error:

Error in getBM(attributes = c("ensemblgeneid", "externalgenename"), : 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

The weird fact is that this is not happening everytime, sometimes it does, sometimes it doesn't. I am also trying with different GO numbers and it looks like it doesn't depend on it. For example, I try the first time with the GO x it doesn't work but if I re-try 30 seconds later with exactly the same command it works perfectly. I don't know how to figure it out this. I already tried changing the host but it didn't help. Any suggestions?

Cheers,

Lorena

biomart R ensembl bioconductor • 64 views
ADD COMMENTlink written 23 days ago by lbuo0

How did you try changing the host? Using one of the mirror sites is usually my go-to solution for this.

ADD REPLYlink written 23 days ago by Mike Smith3.8k
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