Package ubic.basecode.math.linearmodels

Class LeastSquaresFitTest

java.lang.Object

ubic.basecode.math.linearmodels.LeastSquaresFitTest

public class LeastSquaresFitTest
extends Object

Author:

paul

Constructor Summary

Constructors

Constructor	Description
LeastSquaresFitTest()

Method Summary

Modifier and Type	Method	Description
void	testEstrogen()	Tests limma-like functionality.
void	testLSFOneContinuousWithMissing3()
void	testLSFThreeLevelsOnecontinous2()
void	testLSFThreeLevelsOneContinuousWithMissing3()
void	testLSFTwoLevels()
void	testLSFTwoLevels2()	Many missing values; Two factors, two levels + interaction.
void	testLSFTwoLevels3()
void	testLSFTwoLevelsOneContinuous()
void	testMatrixWeightedRegress()	Weighted least squares test for 2D matrices
void	testNHBE()	Tests limma-like functionality Multiple levels per factor, unbalanced design
void	testOneWayAnova()	Has a lot of missing values.
void	testSingular()
void	testSingular2()	Originally causes failures during summarization step.
void	testThreeWaySingular()
void	testTwoWayAnovaUnfittable()	Sanity check.
void	testTwoWayAnovaWithInteractions()	Check for problem reported by TF -- Gemma gives slightly different result.
void	testTwoWayTwoLevelsOneContinousInteractionC()	No missing values; Two-way ANOVA with interaction, PLUS a continuous covariate.
void	testVectorRegress()
void	testVectorWeightedRegress()
void	testVectorWeightedRegressWithMissing()

Methods inherited from class java.lang.Object

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

Constructor Detail

LeastSquaresFitTest

public LeastSquaresFitTest()

Method Detail

testLSFOneContinuousWithMissing3

public void testLSFOneContinuousWithMissing3()
                                      throws Exception

Throws:

Exception

testLSFThreeLevelsOnecontinous2

public void testLSFThreeLevelsOnecontinous2()
                                     throws Exception

Throws:

Exception

testLSFThreeLevelsOneContinuousWithMissing3

public void testLSFThreeLevelsOneContinuousWithMissing3()
                                                 throws Exception

Throws:

Exception

testLSFTwoLevels

public void testLSFTwoLevels()
                      throws Exception

Throws:

Exception

testLSFTwoLevels2

public void testLSFTwoLevels2()
                       throws Exception

Many missing values; Two factors, two levels + interaction.

Throws:

Exception

testLSFTwoLevels3

public void testLSFTwoLevels3()
                       throws Exception

Throws:

Exception

testLSFTwoLevelsOneContinuous

public void testLSFTwoLevelsOneContinuous()
                                   throws Exception

Throws:

Exception

testMatrixWeightedRegress

public void testMatrixWeightedRegress()
                               throws Exception

Weighted least squares test for 2D matrices

Throws:

Exception

testOneWayAnova

public void testOneWayAnova()
                     throws Exception

Has a lot of missing values.

Throws:

Exception

testSingular

public void testSingular()
                  throws Exception

Throws:

Exception

testSingular2

public void testSingular2()
                   throws Exception

Originally causes failures during summarization step. There are two pivoted columns.

Throws:

Exception

testThreeWaySingular

public void testThreeWaySingular()
                          throws Exception

Throws:

Exception

testTwoWayAnovaUnfittable

public void testTwoWayAnovaUnfittable()
                               throws Exception

Sanity check.

Throws:

Exception

testTwoWayAnovaWithInteractions

public void testTwoWayAnovaWithInteractions()
                                     throws Exception

Check for problem reported by TF -- Gemma gives slightly different result. Problem is not at this level.

Throws:

Exception

testTwoWayTwoLevelsOneContinousInteractionC

public void testTwoWayTwoLevelsOneContinousInteractionC()
                                                 throws Exception

No missing values; Two-way ANOVA with interaction, PLUS a continuous covariate.

Throws:

Exception

testVectorRegress

public void testVectorRegress()

testVectorWeightedRegress

public void testVectorWeightedRegress()
                               throws Exception

Throws:

Exception

testVectorWeightedRegressWithMissing

public void testVectorWeightedRegressWithMissing()
                                          throws Exception

Throws:

Exception

testNHBE

public void testNHBE()
              throws Exception

Tests limma-like functionality Multiple levels per factor, unbalanced design

Throws:

Exception

testEstrogen

public void testEstrogen()
                  throws Exception

Tests limma-like functionality. Balanced 2x2 design

Throws:

Exception