Search
Question: getBM query to useEnsembl(biomart="snp"..) not responding
0
gravatar for phpaul2010
5 weeks ago by
phpaul20100
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. 

Suggestions? 

library(biomaRt)

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",
                          'ensembl_gene_stable_id','ensembl_transcript_stable_id'), 
             filters = 'snp_filter', values =px, mart = variation)

 

ADD COMMENTlink modified 4 weeks ago by Mike Smith2.1k • written 5 weeks 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 4 weeks ago by Mike Smith2.1k
0
gravatar for Mike Smith
4 weeks ago by
Mike Smith2.1k
EMBL Heidelberg / de.NBI
Mike Smith2.1k wrote:

This should now be fixed (https://groups.google.com/forum/?fromgroups#!topic/biomart-users/ckiglj9Og6A)

ADD COMMENTlink written 4 weeks ago by Mike Smith2.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 223 users visited in the last hour