trans.main
Class WilcoxonRankSumTest

java.lang.Object
  trans.main.WilcoxonRankSumTest

public class WilcoxonRankSumTest

extends java.lang.Object

Implementation of a Wilcoxon Rank Sum Test. Note, if the number of samples for either the treatment or control group is <10, no test statistics are calculated and the pValue is set to 1, logTPvalue is set to 0, and z to -10.

Constructor Summary

WilcoxonRankSumTest()

Method Summary

double	calculateZ() Only valid when # treatment samples and # control samples >9 each.
double	getLogTPvalue()
int	getNumberTreatmentsControls()
static void	main(java.lang.String[] args)
void	makeSamples(float[][] treatment, float[][] control, int startIndex, int stopIndex) Builds samples from part of a float[replica][intensities] for treat and control.
void	makeSamples(float[] treatment, float[] control)
void	rankSamples() Ranks a sorted array of WilcoxonSamples based on value.
void	setTwoTailed(boolean twoTailed)
void	sumRanks()
double	test(float[][] treatment, float[][] control, int startIndex, int stopIndex) Returns a -10LogBase10(pValue) if n1 and n2 >9
double	test(float[] treatment, float[] control) Returns a -10LogBase10(pValue) if n1 and n2 >9.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

WilcoxonRankSumTest

public WilcoxonRankSumTest()

Method Detail

test

public double test(float[] treatment,
                   float[] control)

Returns a -10LogBase10(pValue) if n1 and n2 >9. if twoTailed is true and z is neg, will return a - logTPValue.

test

public double test(float[][] treatment,
                   float[][] control,
                   int startIndex,
                   int stopIndex)

Returns a -10LogBase10(pValue) if n1 and n2 >9

calculateZ

public double calculateZ()

Only valid when # treatment samples and # control samples >9 each.

sumRanks

public void sumRanks()

rankSamples

public void rankSamples()

Ranks a sorted array of WilcoxonSamples based on value. If no ties are found then this is simply their array index number+1. (ie 1,2,3,4...) If ties are encountered, ties are assigned the average of their index positions+1. (ie if index+1's: 2,3,4 have the same absolute difference, all are assigned a rank of 3).

makeSamples

public void makeSamples(float[] treatment,
                        float[] control)

makeSamples

public void makeSamples(float[][] treatment,
                        float[][] control,
                        int startIndex,
                        int stopIndex)

Builds samples from part of a float[replica][intensities] for treat and control.

main

public static void main(java.lang.String[] args)

getLogTPvalue

public double getLogTPvalue()

getNumberTreatmentsControls

public int getNumberTreatmentsControls()

setTwoTailed

public void setTwoTailed(boolean twoTailed)