Error in BioMartVersion

Question

[hodayabeer]

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!

[GenoMax]

When calling web services via a loop one should build a sleep/wait time to prevent going over maximum connections allowed by the site over unit time (e.g. https://github.com/Ensembl/ensembl-rest/wiki/Rate-Limits ).

[Mike Smith]

Can you update your post to include the output of sessionInfo() so we can see which versions of R and biomaRt you're using? I suspect your package is a little out of data, www.biomart.org hasn't been the relevant website to check for quite a while & that error message is no longer in the current version of the package.

Answer 1

[James Ashmore]

A slightly easier and faster method would be to use the annotation packages Bioconductor provides:

library("org.Hs.eg.db")
entrez <- c("100422954", "100422957", "100422959", "100422962")
symbol <- mapIds(org.Hs.eg.db, keys = entrez, keytype = "ENTREZID", column = "SYMBOL")