halo.normalization
Class Normalization

java.lang.Object
  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