[ensembl-dev] get Illumina probesets via api

Nathan Johnson njohnson at ebi.ac.uk
Fri Apr 27 13:08:56 BST 2012

Hi David

You are right in that you need to handle probe and probesets independently, this has always been the case.

You could potentially have a single point of access if you use the DBEntryAdaptor directly:


However, this would get all the DBEntry objects for that transcript, and you would have to filter out the Probe/ProbeSet entries and then fetch them via their respective adaptors. I think this is a much less efficient way of accessing the data, but does make information about the xref available via DBEntry->linkage_annotation.

If you haven't already seen the examples script, you can find it here:


I hope this helps.



On 27 Apr 2012, at 12:54, David Bauer wrote:

> Answer to myself:
> These are probes and not probesets. So one must use the probe adapter.
> This was different in earlier versions of the funcgen api.
> The current implementation is cleaner but also more confusing ;-)
> Kind regards,
> David.
> Von: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org]
> Gesendet: Freitag, 27. April 2012 12:44
> An: Ensembl developers list (dev at ensembl.org)
> Betreff: [ensembl-dev] get Illumina probesets via api
> Hi,
> I’m trying to get Illumina probesets mapped to a transcript via
> my @probesets = @{$pba->fetch_all_by_linked_Transcript($transcript)}
> This gives me all probesets from the various Affy chips but the Illumina, Codelink and Phalanx (displayed on the web page) are missing.
> Is there some different api call I must use to get those mappings ? (using version 66)
> Kind regards,
> David.
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Nathan Johnson
Senior Scientific Programmer
Ensembl Regulation
European Bioinformatics Institute
Wellcome Trust Genome Campus
Cambridge CB10 1SD


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