[BioC] biomaRt- too many attributes selected

Lavinia Gordon lavinia.gordon at mcri.edu.au
Fri Jun 3 04:07:46 CEST 2011

Dear biomaRt users,

Following a simple query like Task 2 in the biomaRt users guide 

getBM(attributes = myattributes, filters = "entrezgene", values = 
entrez,mart = ensembl)

I am running into an issue with this error:
Error in getBM(attributes = myattributes, filters = "entrezgene", values 
= entrez,  :
   Query ERROR: caught BioMart::Exception::Usage: Too many attributes 
selected for External References

where myattributes =
[1] "mim_morbid_accession"   "mim_morbid_description" 
"mim_gene_accession"     "mim_gene_description"

and entrez =
[1] "673" "837"

Is there anyway around this error rather than just running two queries? 
I am surprised that four attributes are considered too many.

With thanks for your help,

Lavinia Gordon.

 > sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-pc-mingw32/i386 (32-bit)

[1] LC_COLLATE=English_Australia.1252  
LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252 
LC_NUMERIC=C                       LC_TIME=English_Australia.1252

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

other attached packages:
[1] biomaRt_2.6.0          limma_3.6.9            hgu133plus2probe_2.7.0 
AnnotationDbi_1.12.0   hgu133plus2cdf_2.7.0   gcrma_2.22.0           
affy_1.28.0            Biobase_2.10.0

loaded via a namespace (and not attached):
  [1] affyio_1.18.0         Biostrings_2.18.4     DBI_0.2-5             
IRanges_1.8.9         preprocessCore_1.12.0 RCurl_1.5-0.1         
RSQLite_0.9-4         splines_2.12.0        tools_2.12.0          

Senior Bioinformatics Officer
Murdoch Childrens Research Institute
Royal Children's Hospital
Flemington Road
Victoria 3052

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