Changes between Version 4 and Version 5 of Ticket #541, comment 4


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Timestamp:
Dec 3, 2013, 2:14:22 PM (11 years ago)
Author:
olle

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  • Ticket #541, comment 4

    v4 v5  
    22
    33 * Class `QuantileNormalization` in `src/net/sf/basedb/plugins/QuantileNormalization.java` extends `AbstractNormalizationPlugin`, and the latter contains several methods to access data, all using method `VirtualColumn.channelIntensity(int channel)` to retrieve the data from the database. For transformed data in log-2 or log-10 format, this means that the data is returned in untransformed format, and will be stored as such after normalization.
    4  * Exchanging method `VirtualColumn.channelIntensity(int channel)` calls in class `AbstractNormalizationPlugin` for `VirtualColumn.channelRaw(int channel)` calls, will result in the data being returned as stored in the database, without any optional transformation, and therefore will be stored after normalization in the same format as when fetched.
     4 * Exchanging method `VirtualColumn.channelIntensity(int channel)` calls in class `AbstractNormalizationPlugin` for `VirtualColumn.channelRaw(int channel)` calls, will result in the data being returned as stored in the database, without any optional transformation, and therefore will be stored after normalization in the same format as when fetched. For this to work, it is essential that a proper averaging method is used, as e.g. using geometric mean for data with zero or negative values leads to problems.