The query to the BioMart webservice returned an invalid result: biomaRt expected a character string
0
0
Entering edit mode
lbuo • 0
@lbuo-21134
Last seen 2.2 years ago

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 ensembl R Bioconductor • 329 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 479 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