Opened 12 years ago

Closed 12 years ago

Last modified 33 hours ago

#247 closed defect (fixed)

net.sf.basedb.normalizers: qQuantileNormalization crashes when normalizing filtered bioassay sets

Reported by: Jari Häkkinen Owned by: Jari Häkkinen
Priority: major Milestone: ZZ Normalization package v1.1
Component: net.sf.basedb.examples.extensions Keywords:
Cc:

Description

When qQuantiler normalizes bioassay sets where assays have been removed by a filter the plug-in crashes. The problems is traced to the deprecated exportPlainMatrix method of BioAssaySetExporter class. exportPlainMatrix will not be fixed so the underlying C++ binary must be extended to work around the exportPlainMatrix problem.

exportPlainMatrix will add emtpy filed for filtered out assays, i.e., it does not export the actual bioassay set. The reason for this is a flaw in matrix creation code in exportPlainMatrix where internal assay id's are used rather than the actual list of assays.

When ticket:183 is resolved the work around in qQN.cc can be removed.

Change History (3)

comment:1 Changed 12 years ago by Jari Häkkinen

Status: newassigned

comment:2 Changed 12 years ago by Jari Häkkinen

Resolution: fixed
Status: assignedclosed

(In [1164]) Fixes #247. A work around for the erroneous export from exportPlainMatrix.

comment:3 Changed 33 hours ago by Nicklas Nordborg

Milestone: Normalization package v1.1ZZ Normalization package v1.1

Milestone renamed

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