Class MedianRatioNormalization

    • Constructor Detail

      • MedianRatioNormalization

        public MedianRatioNormalization()
    • Method Detail

      • run

        public void run​(Request request,
                        Response response,
                        ProgressReporter progress)
        Description copied from interface: Plugin
        Run the plugin. If a progress reporter object is passed it is recommended that the plugin makes use of it.
        Specified by:
        run in interface Plugin
        Parameters:
        request - Request object with the command and parameters
        response - Response object in for the plugin to response through
        progress - A ProgressReporter where the plugin can report its progess, can be null
      • getSignalHandler

        public SignalHandler getSignalHandler()
        Description copied from interface: SignalTarget
        Get the signal handler that is handling signals on behalf of this object. Multiple invokations of this method may receive the same or different objects. Null may be returned if, for some reason, the current object instance doesn't want to receive signals. Returning null is the same as not implementing this interface.
        Specified by:
        getSignalHandler in interface SignalTarget
        Returns:
        A SignalHandler object, or null if the current instance doesn't support signals
      • normalize1ch

        private BioAssaySet normalize1ch​(DbControl dc,
                                         BioAssaySet source,
                                         Job job,
                                         float minIntensity,
                                         float lowExclude,
                                         float highExclude,
                                         ProgressReporter progress)
        Normalise the source bioassay set using MEDIAN-RATIO normalization.
        Parameters:
        dc - The DbControl to use for database access
        source - The source bioassay set that is going to be normalized
        job - The job in which the normalization is done.
        minIntensity - All spots which have a lower intensity value in either channel will be filtered out
        lowExclude - A percentage of the spots with lowest ratio that are excuded in the median calculation
        highExclude - A percentage of the spots with highest ratio that are excluded in the median calculation
        progress - Progress reporter for the caller to keep track of the plugin's progress. Null is allowed.
        Returns:
        The normalized bioassayset
        Since:
        2.7, 3.2.4 (removed scale parameter)
      • normalize

        public BioAssaySet normalize​(DbControl dc,
                                     BioAssaySet source,
                                     Job job,
                                     float minIntensity,
                                     float lowExclude,
                                     float highExclude,
                                     int blockGroupSize,
                                     ProgressReporter progress)
        Normalise the source bioassay set using MEDIAN-RATIO normalization. NOTE! This normalization method only works with 2-channel data.
        Parameters:
        dc - The DbControl to use for database access
        source - The source bioassay set that is going to be normalized
        job - The job that is doing the normalization, or null
        minIntensity - All spots which have a lower intensity value in either channel will be filtered out
        lowExclude - A percentage of the spots with lowest ratio that are excuded in the median calculation
        highExclude - A percentage of the spots with highest ratio that are excluded in the median calculation
        progress - Progress reporter for the caller to keep track of the plugin's progress. Null is allowed.
        Returns:
        The normalized bioassayset
        Since:
        2.5; This method was removed in 2.7.0 by accident, added in 2.7.2 again
      • median

        private float median​(float[] sortedArray,
                             int first,
                             int last)