Changes between Version 3 and Version 4 of Ticket #541, comment 2


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Timestamp:
Dec 3, 2013, 1:44:29 PM (10 years ago)
Author:
olle

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  • Ticket #541, comment 2

    v3 v4  
    22
    33 1. Originally data in BASE was stored in untransformed format, and the average method used was arithmetic mean (the latter differs from the current recommendation for untransformed data, which is to use geometric mean).
    4  2. A flag indicating if stored data was untransformed, stored as log-2, or log-10 values, was introduced in BASE Ticket [http://base.thep.lu.se/ticket/1120 #1120] (The dynamic part of BASE should keep track whether intensity data is in log space or not). See this ticket for a lengthy discussion on the use and storage of transformed data in BASE. Some additions were:[[BR]][[BR]]a. A `BioAssaySet` has a `getIntensityTransform()` method that returns an `IntensityTransform` `enum` object, whose public `Formula.AverageMethod getAverage()` method returns `Formula.AverageMethod.ARITHMETIC_MEAN` or `Formula.AverageMethod.GEOMETRIC_MEAN`.[[BR]]b. Class `VirtualColumn` was extended with static methods `VirtualColumn channelIntensity(int channel)` and `VirtualColumn channelRaw(int channel)`. The former performs a reverse transformation, determined by the transformation flag, in order to return untransformed data, while the latter returns data the way it was stored in the database, i.e. data in log-2 and log-10 format is returned in that format.[[BR]][[BR]]
     4 2. A flag indicating if stored data was untransformed, stored as log-2, or log-10 values, was introduced in BASE Ticket [http://base.thep.lu.se/ticket/1120 #1120] (The dynamic part of BASE should keep track whether intensity data is in log space or not). See this ticket for a lengthy discussion on the use and storage of transformed data in BASE. Some additions were:[[BR]][[BR]]a. A `BioAssaySet` has a `getIntensityTransform()` method that returns an `IntensityTransform` `enum` object, whose public `Formula.AverageMethod getAverage()` method returns `Formula.AverageMethod.ARITHMETIC_MEAN` or `Formula.AverageMethod.GEOMETRIC_MEAN`.[[BR]]b. Class `VirtualColumn` was extended with static methods `VirtualColumn channelIntensity(int channel)` and `VirtualColumn channelRaw(int channel)`. The former performs a reverse transformation if needed, determined by the transformation flag, in order to return untransformed data, while the latter returns data the way it was stored in the database, i.e. data in log-2 and log-10 format is returned in that format.[[BR]][[BR]]
    55 3. Enum class `IntensityTransform` public `Formula.AverageMethod getAverage()` method does however return `Formula.AverageMethod.ARITHMETIC_MEAN` for data stored in untransformed format (according to the flag), and `Formula.AverageMethod.GEOMETRIC_MEAN` for data stored in log-2 or log-10 format. This is the opposite to what is recommended to be used in this ticket, for data fetched in untransformed form.