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? Thanks, Mark Mark W. Kimpel MD ? Official Business Address: ? Department of Psychiatry Indiana University School of Medicine Biotechnology, Research, & Training Center 1345 W. 16th Street Indianapolis, IN 46202 ? Preferred Mailing Address: ? 15032 Hunter Court Westfield, IN? 46074 ? (317) 490-5129 Home, Work, & Mobile 1-(317)-536-2730 FAX

On Jun 22, 2005, at 2:20 PM, Kimpel, Mark W wrote: > 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, When mapping within the same species, you need specify only the from.species (and specifying a to.species as the same species will lead to an error--we should fix this with a warning....). The next issue is the possible values for xrefs. The function getPossibleXrefs(mart) will give you the possible xrefs sorted by species. With ensembl mart 31, they have gone to several different flavors of "refseq". I'm guessing that you want "refseq_dna" as the to.xref. Putting everything together: > getXref(id = "X97772_g_at", from.species = "rnorvegicus", from.xref = "affy_rg_u34a", to.xref = "refseq_dna", mart = mart) An object of class "martTable" Slot "id": [1] "X97772_g_at" Slot "table": $from.id [1] "X97772_g_at" $to.id [1] "NM_031620.1" $martID [1] "ENSRNOG00000019328" Hope this helps, Sean