Uses of Class
halo.normalization.Normalization

Packages that use Normalization
halo.data Provides for the extraction, filtering, handling and saving of expression data. 
halo.normalization Provides for the calculation and handling of normalization. 
halo.userinterface.cmdline Provides for the handling of user input and starting of corresponding calculations. 
halo.userinterface.gui Provides for the generation and handling of a graphical user interface, as well as the starting of corresponding calculations according to user input. 
halo.userinterface.gui.graphhandler Provides for generation of plots and histograms. 
 

Uses of Normalization in halo.data
 

Methods in halo.data with parameters of type Normalization
static Data Filter.filterPQS(Data data, Normalization l, boolean histogram)
          Please note that this method can only be used after normalization!
static Data Filter.filterPQS(Data data, Normalization l, double threshold, boolean histogram)
          Please note that this method can only be used after normalization!
static Data Filter.filterPQS(Data data, Normalization l, int replicate, boolean histogram)
          Please note that this method can only be used after normalization!
 

Uses of Normalization in halo.normalization
 

Subclasses of Normalization in halo.normalization
 class LinearRegression
          Implementation of normalization method=linear regression based on simple linear regression Command line option: -l standard
 

Uses of Normalization in halo.userinterface.cmdline
 

Methods in halo.userinterface.cmdline that return Normalization
static Normalization CmdFilterData.performNormalization(Data data)
          Performs normalization on a given Data object with the previously specified method
 

Uses of Normalization in halo.userinterface.gui
 

Methods in halo.userinterface.gui that return Normalization
 Normalization GuiNormal.getNormalization()
          Returns the normalization Object
 

Methods in halo.userinterface.gui with parameters of type Normalization
 void GuiFilterData.setNorm(Normalization norm)
          Sets the normalization object needed for evaluation
 

Uses of Normalization in halo.userinterface.gui.graphhandler
 

Methods in halo.userinterface.gui.graphhandler with parameters of type Normalization
static XYGraphConstructor GraphHandler.plotNormalization(Normalization norm, Data data)
          Generates the plot for normalization