halo.normalization
Class Normalization

java.lang.Object
  extended by halo.normalization.Normalization
Direct Known Subclasses:
LinearRegression

public abstract class Normalization
extends java.lang.Object

Provides methods for normalization and retrieving of correction factors

Author:
Stefanie Kaufmann

Field Summary
static int UNDEF
           
 
Constructor Summary
Normalization()
           
 
Method Summary
abstract  CorrectionFactors calculateCorrectionFactors()
          calculates correction factors via normalization methods
 CorrectionFactors calculateCorrectionFactors(int replicate)
          Calculates the correction factors for a certain replicate
 double[] calculateQualityControl(Data data, boolean histogram)
          Calculates the array containing the quality control values; these are calculated as distance from the normalization line
 void generateHistogram(double[] pqs, double max)
          Uses the PQS data and generates a histogram from it
 double getAlpha()
          Returns the factor alpha from normalization
 double getBeta()
          Returns the factor beta from normalization
 CorrectionFactors getCorr()
          Returns the correction factors
 double getPqsMax()
          Returns the highest value of the probe set quality scores
 int getReplicate()
          Returns the replicate for calculation
 void setCorr(CorrectionFactors corr)
          Sets the correction factors
 void setReplicate(int replicate)
          Sets the replicate for calculation
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

UNDEF

public static final int UNDEF
See Also:
Constant Field Values
Constructor Detail

Normalization

public Normalization()
Method Detail

calculateCorrectionFactors

public abstract CorrectionFactors calculateCorrectionFactors()
calculates correction factors via normalization methods

Returns:
Correction factors c_u, c_l and c_lu

calculateCorrectionFactors

public CorrectionFactors calculateCorrectionFactors(int replicate)
Calculates the correction factors for a certain replicate

Parameters:
replicate - The replicate for which the correction factors will be calculated
Returns:
The Correction factors for this replicate

calculateQualityControl

public double[] calculateQualityControl(Data data,
                                        boolean histogram)
Calculates the array containing the quality control values; these are calculated as distance from the normalization line

Parameters:
data - The data object containing the RNA values
histogram - TRUE if a histogram should be created for the quality scores, FALSE otherwise
Returns:
probe-set quality control values

generateHistogram

public void generateHistogram(double[] pqs,
                              double max)
Uses the PQS data and generates a histogram from it

Parameters:
pqs - The probe-set quality control values
max - The maximum value among these (for definition of the x-range)

setCorr

public void setCorr(CorrectionFactors corr)
Sets the correction factors

Parameters:
corr - The correction factors

setReplicate

public void setReplicate(int replicate)
Sets the replicate for calculation

Parameters:
replicate - The replicate for calculation

getAlpha

public double getAlpha()
Returns the factor alpha from normalization

Returns:
The factor alpha

getBeta

public double getBeta()
Returns the factor beta from normalization

Returns:
The factor beta

getCorr

public CorrectionFactors getCorr()
Returns the correction factors

Returns:
The correction factors

getPqsMax

public double getPqsMax()
Returns the highest value of the probe set quality scores

Returns:
The highest value of the probe set quality scores

getReplicate

public int getReplicate()
Returns the replicate for calculation

Returns:
The replicate for calculation