Changes between Version 2 and Version 3 of Ticket #228, comment 9


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Timestamp:
Dec 9, 2013, 10:09:39 AM (11 years ago)
Author:
olle

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  • Ticket #228, comment 9

    v2 v3  
    11Problem discussion update:
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    3  * BASE Ticket [http://base.thep.lu.se/ticket/1792 #1792] (Incorrect average method specified in !IntensityTransform) switched the results returned by public method `Formula.AverageMethod getAverage()` in enum class `IntensityTransform` for data flagged to be stored in untransformed, relative to transformed (log-2 or log-10) format (see changeset [http://base.thep.lu.se/changeset/6364 [6564]]):[[BR]][[BR]]`Formula.AverageMethod.GEOMETRIC_MEAN` for data stored in untransformed format[[BR]]`Formula.AverageMethod.ARITHMETIC_MEAN` for data stored in transformed format[[BR]][[BR]]This would solve the problem with wrong default averaging method being shown for `QuantileNormalizer`. However, there are benefits letting the plug-in itself determine the default averaging method, based on the intensity transform information for the `BioAssaySet` to work on.
     3 * BASE Ticket [http://base.thep.lu.se/ticket/1792 #1792] (Incorrect average method specified in !IntensityTransform) switched the results returned by public method `Formula.AverageMethod getAverage()` in enum class `IntensityTransform` for data flagged to be stored in untransformed, relative to transformed (log-2 or log-10) format (see changeset [http://base.thep.lu.se/changeset/6364 [6564]]):[[BR]][[BR]]`Formula.AverageMethod.GEOMETRIC_MEAN` for data stored in untransformed format[[BR]]`Formula.AverageMethod.ARITHMETIC_MEAN` for data stored in transformed format[[BR]][[BR]]This would solve the problem with wrong default averaging method being shown for `QuantileNormalizer`. However, there are benefits letting the plug-in itself determine the default averaging method, based on the intensity transform information for the `BioAssaySet` to work on.[[BR]][[BR]]Class `IntensityTransform` was extended with new public method `double transform(double value)` in changeset [http://base.thep.lu.se/changeset/6365 [6365]], that stores data in the same transform as the source data.
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