Changes between Initial Version and Version 1 of Ticket #228, comment 12


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Timestamp:
Dec 9, 2013, 3:56:04 PM (11 years ago)
Author:
olle

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  • Ticket #228, comment 12

    initial v1  
    11(In [2165]) Refs #228. Refs #541. Quantile normalization updated to untransform logarithmic data before normalization, and then transform it back to logarithmic format before results are stored. Default averaging method will always be set to `Formula.AverageMethod.GEOMETRIC_MEAN`:
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    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.
     3 1. Class/file `QuantileNormalization.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.
    44 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.
    55 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.