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
?
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Department of Psychiatry
Indiana University School of Medicine
Biotechnology, Research, & Training Center
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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
