net.sf.basedb.normalizers: qQuantileNormalization crashes when normalizing filtered bioassay sets
|ZZ Normalization package v1.1
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.