#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 by , 15 years ago
| Status: | new → assigned |
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comment:2 by , 15 years ago
| Resolution: | → fixed |
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| Status: | assigned → closed |
comment:3 by , 4 years ago
| Milestone: | Normalization package v1.1 → ZZ Normalization package v1.1 |
|---|
Milestone renamed
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(In [1164]) Fixes #247. A work around for the erroneous export from exportPlainMatrix.