Question: getBM query to useEnsembl(biomart="snp"..) not responding
gravatar for phpaul2010
12 months ago by
phpaul20100 wrote:

The R script below worked several days ago, for the past two days  it hangs or occasionally returns 

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.

R libraries and biconductor libraries  updated with no effect. 



variation = useEnsembl(biomart="snp", dataset="hsapiens_snp")

px <- c("rs11432677","rs632952","rs60178352","rs174686","rs201456215")

ppx <- getBM(attributes=c('refsnp_id','chr_name','chrom_start','chrom_end',"ensembl_peptide_allele",
             filters = 'snp_filter', values =px, mart = variation)


ADD COMMENTlink modified 12 months ago by Mike Smith2.9k • written 12 months ago by phpaul20100

I can confirm I'm experiencing the same issues.  I see the same problem if I use one the Ensembl mirror sites, or the web interface to carry out the query, which suggests to me that it's an issue with the databae, rather than the web interface.  If that's the case then there isn't really anything we can 'fix' in biomaRt, but I'll keep look at the issue.

ADD REPLYlink written 12 months ago by Mike Smith2.9k
gravatar for Mike Smith
12 months ago by
Mike Smith2.9k
EMBL Heidelberg / de.NBI
Mike Smith2.9k wrote:

This should now be fixed (!topic/biomart-users/ckiglj9Og6A)

ADD COMMENTlink written 12 months ago by Mike Smith2.9k
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