Thanks Steffen
That sorted it.
Aedin

sdurinck@ebi.ac.uk wrote:

>Hi Aedin,
>
>You should upgrade biomaRt and use the latest version (1.5.10, see
>developmental packages).
>
>Best,
>Steffen
>
>  
>
>>Dear BioC and Steffen
>>I'd be grateful for your help.  I getting an xmlTreeParse error with
>>useDataset()
>>Thanks
>>Aedin
>>
>> > listDatasets(mart)
>>                      dataset    version
>>1      mmusculus_gene_ensembl    NCBIM34
>>2  tnigroviridis_gene_ensembl TETRAODON7
>>3      frubripes_gene_ensembl      FUGU4
>>4  dmelanogaster_gene_ensembl      BDGP4
>>5        ggallus_gene_ensembl    WASHUC1
>>6    scerevisiae_gene_ensembl       SGD1
>>7       agambiae_gene_ensembl     AgamP3
>>8     mdomestica_gene_ensembl    BROADO2
>>9    rnorvegicus_gene_ensembl    RGSC3.4
>>10    amellifera_gene_ensembl    AMEL2.0
>>11       btaurus_gene_ensembl   Btau_2.0
>>12 cintestinalis_gene_ensembl       JGI2
>>13      celegans_gene_ensembl     CEL150
>>14      hsapiens_gene_ensembl     NCBI35
>>15   xtropicalis_gene_ensembl       JGI4
>>16   cfamiliaris_gene_ensembl    BROADD1
>>17      mmulatta_gene_ensembl   MMUL_0_1
>>18  ptroglodytes_gene_ensembl    CHIMP1A
>>19        drerio_gene_ensembl     ZFISH5
>>
>> > mart<-useDataset(dataset="hsapiens_gene_ensembl", mart=mart)
>>Reading database configuration of: hsapiens_gene_ensembl
>>Entity: line 1: parser error : Start tag expected, '<' not found
>>NA
>>^
>>Error in .Call("RS_XML_ParseTree", as.character(file), handlers,
>>as.logical(ignoreBlanks),  :
>>        error in creating parser for NA
>>
>> > traceback()
>>3: .Call("RS_XML_ParseTree", as.character(file), handlers,
>>as.logical(ignoreBlanks),
>>       as.logical(replaceEntities), as.logical(asText), as.logical(trim),
>>       as.logical(validate), as.logical(getDTD), as.logical(isURL),
>>       as.logical(addAttributeNamespaces), as.logical(useInternalNodes),
>>       FALSE, as.logical(isSchema))
>>2: xmlTreeParse(res[1, ])
>>1: useDataset(dataset = "hsapiens_gene_ensembl", mart = mart)
>>
>> > sessionInfo()
>>R version 2.2.0, 2005-10-06, i686-redhat-linux-gnu
>>
>>attached base packages:
>>[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
>>[7] "base"
>>
>>other attached packages:
>> biomaRt      XML   RMySQL      DBI
>> "1.4.0" "0.99-6"  "0.5-7" "0.1-10"
>>
>>_______________________________________________
>>Bioconductor mailing list
>>Bioconductor@stat.math.ethz.ch
>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
>>    
>>
>
>  
>


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