Opened 10 years ago

Closed 10 years ago

Last modified 10 years ago

#217 closed task (fixed)

GCT exporter

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: ZZ GenePattern integration v1.0
Component: net.sf.basedb.genepattern Keywords:
Cc:

Description

Create an exporter that can export a bioassay set to GCT format. This file format is used as input to lots of GenePattern? modules and is essential before further functionality can be developed. It should not be very difficult since there is a good description at http://www.broad.mit.edu/cancer/software/genepattern/tutorial/gp_fileformats.html#gct

One thing to note is that genes/reporters must be unique, which means that we must always merge on reporter when exporting to this format. Support for this already exists in the AbstractBioAssaySetExporter class.

Change History (3)

comment:1 Changed 10 years ago by Nicklas Nordborg

Status: newassigned

comment:2 Changed 10 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

(In [1091]) Fixes #217: GCT exporter

comment:3 Changed 10 years ago by Nicklas Nordborg

(In [1092]) References #217: GCT exporter

Make sure assay names are unique in the GCT file

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