[ensembl-dev] Get Oligo probes
Sébastien Moretti
sebastien.moretti at unil.ch
Tue Apr 1 08:50:17 BST 2014
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/
More information about the Dev
mailing list