biomaRt server is down
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eb3069 • 0
@eb3069-17541
Last seen 3.2 years ago

This link for bioMart available marts is down (http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt) which is causing the "Unexpected format to the list of available marts" error.  When can I expect the webpage to be fixed?  Thanks!

This is the code:

tx2g <- function(){
  library("biomaRt")
  mart <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = ensembl_dataset)
  t2g <- biomaRt::getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id",
                                         "external_gene_name"), mart = mart)
  t2g <- dplyr::rename(t2g, target_id = ensembl_transcript_id,
                         ens_gene = ensembl_gene_id, ext_gene = external_gene_name)
  return(t2g)
}
t2g <- tx2g()

 

It usually works fine, but this error is a somewhat frequent problem for me.

Thanks again,

Eve

biomart problem with connection • 879 views
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@james-w-macdonald-5106
Last seen 3 hours ago
United States

You can always use the local mirror.

> mart <- useMart("ensembl","hsapiens_gene_ensembl")
Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE,  :
  Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
> mart <- useMart("ensembl","hsapiens_gene_ensembl", host = "useast.ensembl.org")
> getBM("ensembl_gene_id", "hgnc_symbol", "BRCA1", mart)
  ensembl_gene_id
1 ENSG00000012048
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Thanks, this seems to have worked

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