All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`void`	`calculateMetrics()`
`long`	`getCrossHybridizationRejections()`	Use after analysis.
`DoubleArrayList`	`getHistogramArrayList()`
`ObjectArrayList`	`getKeepers()`
`QuantitationType`	`getMetricType()`
`double`	`getNumUniqueGenes()`
`CompositeSequence`	`getProbeForRow(ExpressionDataMatrixRowElement rowEl)`
`double`	`getScoreInBin(int i)`
`int`	`numCached()`
`void`	`setDuplicateMap(Map<CompositeSequence,Set<Gene>> probeToGeneMap)`
`void`	`setLowerTailThreshold(double k)`
`void`	`setMinNumpresent(int minSamplesToKeepCorrelation)`
`void`	`setOmitNegativeCorrelationLinks(boolean omitNegativeCorrelationLinks)`
`void`	`setPValueThreshold(double k)`
`void`	`setUpperTailThreshold(double k)`
`void`	`setUseAbsoluteValue(boolean k)`
`void`	`setUsePvalueThreshold(boolean useIt)`	Default is true; set to false to disable use of the pvalue threshold, in which case only the upper and lower tail thresholds will be used.
`int`	`size()`

DoubleArrayList getHistogramArrayList()

CompositeSequence getProbeForRow(ExpressionDataMatrixRowElement rowEl)

void setDuplicateMap(Map<CompositeSequence,Set<Gene>> probeToGeneMap)

void setLowerTailThreshold(double k)

void setMinNumpresent(int minSamplesToKeepCorrelation)

void setOmitNegativeCorrelationLinks(boolean omitNegativeCorrelationLinks)

void setUpperTailThreshold(double k)

void setUseAbsoluteValue(boolean k)

Interface MatrixRowPairAnalysis