| 3 | | 1. Class/file `QuantileNormalizer.java` in `src/net/sf/basedb/plugins/` in package `net.sf.basedb.normalizers` updates:[[BR]]a. Private method `RequestInformation getConfiguredJobParameters()` updated to always set the default averaging method to `Formula.AverageMethod.GEOMETRIC_MEAN`.[[BR]]b. Private method `BioAssaySet normalize(DbControl dc, BioAssaySet source, Job job, ProgressReporter progress)` updated to call public method `double transform(double value)` in class `IntensityTransform` to transform the normalized result back before storing it. Error message when number of spots differ between two `BioAssay` sets updated to report the names of the latter and the number of spots in each one. Also minor updates in order to increase clarity of code. |
| 4 | | 3. Class/file `AbstractNormalizationPlugin.java` in `src/net/sf/basedb/plugins/` in package `net.sf.basedb.normalizers` updated in help text for selecting averaging method by avoiding reference to the format data is stored in, since averaging is performed on untransformed data. |
| 5 | | 4. XML files `extensions.xml` in `META-INF` in package `net.sf.basedb.normalizers` updated in help text for `Quantile normalization` by adding information that data stored in logarithmic format will be untransformed before averaging, and then transformed back to logarithmic format before results are stored. |
| | 3 | 1. Data stored in logarithmic format should be untransformed before averaging, and then transformed back to logarithmic format before results are stored. The first part is already implemented by use of static method `VirtualColumn channelIntensity(int channel)` in class `AbstractNormalizationPlugin`, while public method `double transform(double value)` in class `IntensityTransform` should be used to transform the normalized result back before storing results. |
| | 4 | 2. Since averaging is performed on untransformed data, default averaging method should always be set to `Formula.AverageMethod.GEOMETRIC_MEAN`. |
| | 5 | 3. Help text for selecting averaging method in class `AbstractNormalizationPlugin` should be updated to avoid references to the format data is stored in, since averaging is performed on untransformed data. |
| | 6 | 4. Help text for `Quantile normalization` in `META-INF/extensions.xml` should be extended with information that data stored in logarithmic format will be untransformed before averaging, and then transformed back to logarithmic format before results are stored. |
