
Dear BioC list,

I'm getting some very strange behaviour from biomaRt.  The following script works perfectly if I supply a single probe id to the getBM function (i.e. values=probe_ids[1]).  But, when I supply the entire probe_ids list I get the following error.

Error in postForm(paste(mart@host, "?", sep = ""), query = xmlQuery) :
        <not set>

Once I get the above error, I get a whole bunch of new errors for commands that would have worked before the error.
examples:
> annotations=getBM(attributes=c("affy_hg_u133_plus_2", "ensembl_peptide_id","entrezgene", "unified_uniprot_accession", "uniprot_swissprot_accession"), filter="affy_hg_u133_plus_2", values=sample_gene, mart=mart, output="list", na.value="NA")
Error in postForm(paste(mart@host, "?", sep = ""), query = xmlQuery) :
        Couldn't resolve host 'www.biomart.org'

It seems to kill my connection to biomart until I quit R and start all over again.  Can anyone help?  Is there some kind of timeout for such a large query?  Has anyone gotten this sort of thing to work before or can you suggest an alternative way to map all affy probe ids to uniprot IDs in R?

####Start R script#####
#Load the appropriate libraries
library(affy)
library(gcrma)
library("annotate")
library("biomaRt")
library("hgu133plus2")

setwd("/home/my_dir")

#just.gcrma method
#Get file list
celfiles=list.files(path="/home/my_dir")

#Do gcrma normalization
gcrma_exprset=just.gcrma(filenames=celfiles,normalize=TRUE,type="fullmodel",verbose=TRUE,fast=FALSE,optimize.by="memory")

probe_ids=geneNames(gcrma_exprset)

mart <- useMart("ensembl", "hsapiens_gene_ensembl")

annotations=getBM(attributes=c("affy_hg_u133_plus_2", "ensembl_peptide_id","entrezgene", "unified_uniprot_accession", "uniprot_swissprot_accession"), filter="affy_hg_u133_plus_2", values=probe_ids_nc, mart=mart, output="list", na.value="NA")
####End R script#####

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