[ensembl-dev] Get Oligo probes

[Sébastien Moretti]

Hi

I wonder how to retrieve all gene_id and related probeset id for a given 
species and a particular chip type.
Usually I get that from BioMart but cannot find the equivalent way of 
doing that with the Ensembl API
e.g. Ensembl Gene ID 	Affy HG U95AV2 probeset
      ENSG00000261657 	39195_s_at
      ENSG00000234627 	37079_at
      ENSG00000256305 	31325_at
      ...

I tried the method fetch_all_by_linked_transcript_Gene but it fails with 
this error message:
DBD::mysql::db selectcol_arrayref failed: Table 
'homo_sapiens_core_75_37.transcript_stable_id' doesn't exist at 
/usr/local/ensembl/ensembl-funcgen/modules//Bio/EnsEMBL/Funcgen/DBSQL/BaseAdaptor.pm 
line 922.
And the status of the method is "at risk".


Any idea how to do that?
Thanks



PS for the API documentation of fetch_all_by_linked_transcript_Gene() & 
fetch_all_by_linked_Transcript() a '}'  is missing at the end of the 
code example.

-- 
Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4079
http://selectome.unil.ch/ http://bgee.unil.ch/