Error in value[[3L]](cond) : Request to BioMart web service failed.
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methylUser ▴ 10
@methyluser-5943
Last seen 8.0 years ago

Hello, I've been trying to connect to biomart for several times and I am not managing.  Does anyone know a solution to this please?

 

Below is the code I am using to connect:

library("biomaRt")
ensembl = useMart(biomart = "ENSEMBL_MART_ENSEMBL", host = "feb2014.archive.ensembl.org", verbose=TRUE)
ensembl = useDataset("hsapiens_gene_ensembl", mart=ensembl, verbose=TRUE)
filt = c("chromosome_name", "start", "end")
val = list(chromosome_name='10', start_position='6205875', end_position='6205875')
att = c("ensembl_gene_id", "external_gene_id", "gene_biotype", "chromosome_name", "start_position", "end_position")
getBM(attributes=att, filters=filt, values=val, mart=ensembl, verbose=TRUE)

 

Error given:

Error in value[[3L]](cond) :
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.

 

 

biomart • 1.1k views
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This is likely C: Problem with biomart's listMarts function and it's not in our hands -- I have contacted the ensembl help desk.

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