[biomart-users] biomaRt error : Extra Content at the end of document

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[biomart-users] biomaRt error : Extra Content at the end of document

Anthony Colombo
Hi

So a quick search says that the error "extra content at the end of document" is a result of biomaRt being down,  what is the status of biomaRt?  I went to ensembl.org, and things seem to be working.


however when I run, this is a utility function that calls biomaRt..... it generates errors.

 speciesMart<-.findMart(commonNomen)
    speciesSymbol<-"hgnc_symbol"  #hugo nomenclature human only
         message("finding entrez IDs of top ensembl genes...")
         convertedEntrezID<-getBM(filters="ensembl_gene_id",
                    attributes=c("ensembl_gene_id","entrezgene",speciesSymbol,"description"),
                    values=resValues, #fitBundles ensembl Gene Ids
                    mart=speciesMart)




.findMart <- function(commonName=c("human","mouse"),host="www.ensembl.org"){#{{{

  dataset <- switch(match.arg(commonName),
                    human="hsapiens_gene_ensembl",
                    mouse="mmusculus_gene_ensembl")
  useMart("ENSEMBL_MART_ENSEMBL", dataset=dataset, host=host)

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