[BioC] biomaRt getXref problem

[Sean Davis]

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