[BioC] biomaRt getXref problem

Kimpel, Mark W mkimpel at iupui.edu
Wed Jun 22 20:20:42 CEST 2005

I am having difficulty using the getXref function in the package
biomaRt. The script included in the vignette works properly but when I try to use the function to cross-reference certain data types I get error messages. For example:

getXref(id = "X97772_g_at", from.species = "rnorvegicus", to.species = "rnorvegicus",from.xref = "affy_rg_u34a", to.xref = "refseq", mart = mart)

produces the error message

Error in mysqlExecStatement(conn, statement, ...) : 
        RS-DBI driver: (could not run statement: Table 'ensembl_mart_31.rnorvegicus_gene_ensembl__homologs_rnorvegicus__dm' doesn't exist)

I get similar error messages for other cross references, either between or within species. What am I doing wrong?



Mark W. Kimpel MD
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Department of Psychiatry
Indiana University School of Medicine
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