[BioC] biomaRt package: problem with useDataset() function

[Coghlan, Avril]

Dear all,

I am trying to use the biomaRt package to retrieve data from the Ensembl
database.
However, I get an error message using the useDataset() function.
I think this is perhaps because useDataset() does not expect Ensembl
datasets to have spaces in their names, but some do.

I have typed the following to try to select the Mycobacterium ulcerans
dataset from the Ensembl Bacteria database:
   library("biomaRt")
   ensemblbacteria <- useMart("bacterial_mart_9")
   listDatasets(ensemblbacteria)
This tells me that the name of the Mycobacterium ulcerans data set is
"EB 1 m_ulcerans".

However, when I try to select it using useDataset() I get an error
message:
   ensemblMulcerans <- useDataset("EB 1
m_ulcerans",mart=ensemblbacteria)

Error in useDataset("EB 1 m_ulcerans", mart = ensemblbacteria) : 
  The given dataset:  EB 1 m_ulcerans , is not valid.  Correct dataset
names can be obtained with the listDatasets function.

I think this could be because useDataset does not expect dataset names
to contain spaces?


I would be grateful for any help with this.

Kind Regards,
Avril

Avril Coghlan
Cork, Ireland