[BioC] biomaRt xMLTreeParse error
Matt Ritchie
ritchie at ebi.ac.uk
Tue Feb 21 17:32:53 CET 2006
Dear list,
I'm attempting to use the biomaRt library to annotate a microarray data
set, and get the following error message (refer below). This code
(replacing 'ensembl_mart_37' with 'ensembl_mart_36') worked fine a week
ago, so perhaps the latest ENSEMBL release (16/2/6) is causing biomaRt
some trouble?
Many thanks,
Matt Ritchie
> library(biomaRt)
Loading required package: RMySQL
Loading required package: DBI
Loading required package: XML
> listMarts()
[1] "ensembl_mart_37" "vega_mart_37" "snp_mart_37" "msd_mart_4"
[5] "uniprot_mart_17"
> mart<-useMart("ensembl_mart_37")
connected to: ensembl_mart_37
> 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('mmusculus_gene_ensembl', mart=mart)
Reading database configuration of: mmusculus_gene_ensembl
Entity: line 1: parser error : Start tag expected, '<' not found
NA
^
Error in xmlTreeParse(res[1, ]) : error in creating parser for NA
> sessionInfo()
R version 2.2.0, 2005-10-06, i686-pc-linux-gnu
attached base packages:
[1] "methods" "stats" "graphics" "grDevices" "utils" "datasets"
[7] "base"
other attached packages:
biomaRt XML RMySQL DBI fortunes
"1.5.2" "0.97-8" "0.5-5" "0.1-9" "1.2-0"
More information about the Bioconductor
mailing list