Hi,

I am trying to convert between EntrezID to gene symbol using 'bioMart' package and the following function:

source("https://bioconductor.org/biocLite.R")
library('EnrichmentBrowser')
library('biomaRt')

convert_to_genes_symbol<-function(ptwy_genes){
  library('EnrichmentBrowser')
  library('biomaRt')
  #ptwy_name<-get_official_name(names(ptwy_genes))
  ensembl = useEnsembl(biomart="ensembl",dataset="hsapiens_gene_ensembl",GRCh=37)

  entrezIDs2Genes <- getBM(attributes=c('hgnc_symbol','entrezgene'),
                         filters = 'entrezgene',
                         values = ptwy_genes, # a vector containing the EntrezIds to convert
                         mart = ensembl)

  entrezIDs2Genes.ordered <- entrezIDs2Genes
  entrezIDs2Genes.ordered <- entrezIDs2Genes.ordered[order(entrezIDs2Genes.ordered$hgnc_symbol),]
  gene_symbol_list<-entrezIDs2Genes.ordered$hgnc_symbol
  gene_symbol_list<-unique(gene_symbol_list[gene_symbol_list != ""])#remove redundancy and empty elements

  return(gene_symbol_list)#check if returns the appropriate value

}

I have a for loop that calls this function, each time for a different gene list, It worked perfect for about 100 different list of genes, but at some point it outputs the following error:

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.
Error in if (BioMartVersion == "\n" | BioMartVersion == "") { : 
  argument is of length zero

(the link works for me)
this is very strange, especially because I checked the specific gene list were it stops, and tried to apply to it the function manually (out of the for loop), and it worked!

I would very appritiate any idea for a solution to that...

thank you in advance!