[BioC] biomart error

Thu Aug 18 12:02:34 CEST 2011

Dear List,

I am using biomaRt for the first time.

Initially I had problems connecting to hsapiens dataset, though I could 
listMarts. However that issue was resolved (by solutions in some earlier 
posts) by changing the host to www.ensembl.org.

Now though I get the following error message when I try to execute the 
following command:

 >mg_eg.ens.t <- getBM(attributes = 
c("entrezgene","ensembl_gene_id","ensembl_transcript_id","hgnc_symbol"), 
filters = "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = ensembl)

                                                                                                                                      V1
1 <head>
2 <link rel=Shortcut Icon href=/errors/ensembl_ico.png type=image/png />
3 <title>The Ensembl Genome Browser</title>
4 <style type=text/css>
5                 
body{color:#333333;background-color:#eaeeff;font-family:Arial,Helvetica,Sans-serif;font-size:14pt;margin:0;padding:0}
6 
#masthead{color:#ffffff;background-color:#333366;width:100%;height:50px;padding:5px 
0;font-size:1.75em;text-align:center;margin:auto}
Error in getBM(attributes = c("entrezgene", "ensembl_gene_id", 
"ensembl_transcript_id",  :
   The query to the BioMart webservice returned an invalid result: the 
number of columns in the result table does not equal the number of 
attributes in the query. Please report this to the mailing list.

This I found strange as I did the same thing yesterday with another 
object and it worked!!

Full Code and SessionInfo:

head(mg.u.eg$Entrez_Gene_ID)   #[1]     27122      3488        72      
1293 100134134       390

length(mg.u.eg$Entrez_Gene_ID) #[1] 4288

listMarts(host="www.ensembl.org")
ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")
listDatasets(ensembl)
ensembl =  useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", 
dataset="hsapiens_gene_ensembl")
filt = listFilters(ensembl)
atts = listAttributes(ensembl)

mg_eg.ens <- getBM(attributes = 
c("entrezgene","ensembl_gene_id","hgnc_symbol"), filters = "entrezgene", 
values = mg.u.eg$Entrez_Gene_ID, mart = ensembl) # 4016    3

mg_eg.ens.t <- getBM(attributes = 
c("entrezgene","ensembl_gene_id","ensembl_transcript_id","hgnc_symbol"), 
filters = "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = ensembl)

sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
  [5] LC_MONETARY=C              LC_MESSAGES=en_GB.UTF-8
  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biomaRt_2.8.0   DESeq_1.4.1     locfit_1.5-6    lattice_0.19-23
[5] akima_0.5-4     Biobase_2.12.1  WriteXLS_2.1.0  gdata_2.8.2
[9] limma_3.8.2

loaded via a namespace (and not attached):
  [1] annotate_1.30.0      AnnotationDbi_1.14.1 DBI_0.2-5
  [4] genefilter_1.34.0    geneplotter_1.30.0   grid_2.13.0
  [7] gtools_2.6.2         RColorBrewer_1.0-2   RCurl_1.6-4
[10] RSQLite_0.9-4        splines_2.13.0       survival_2.36-5
[13] tools_2.13.0         XML_3.4-0            xtable_1.5-6

Many Thanks,
Natasha

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