ExpressionDataMatrixBuilder (Gemma 1.29.4 API)

java.lang.Object
- ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder

```
public class ExpressionDataMatrixBuilder
extends Object
```
Utility methods for taking an ExpressionExperiment and returning various types of ExpressionDataMatrices, such as the processed data, preferred data, background, etc. This class is not database aware; use the ExpressionDataMatrixService to get ready-to-use matrices starting from an ExpressionExperiment. This handles complexities such as experiments that contain multiple array designs with differing quantitation types.

Author:

pavlidis

Constructor Summary

Constructors
Constructor and Description
`ExpressionDataMatrixBuilder(Collection<? extends DesignElementDataVector> vectors)`
`ExpressionDataMatrixBuilder(Collection<ProcessedExpressionDataVector> processedVectors, Collection<? extends DesignElementDataVector> otherVectors)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`ExpressionDataDoubleMatrix`	`getBackgroundChannelA()`
`ExpressionDataDoubleMatrix`	`getBackgroundChannelB()`
`List<BioAssayDimension>`	`getBioAssayDimensions()`
`ExpressionDataDoubleMatrix`	`getBkgSubChannelA()`
`ExpressionExperiment`	`getExpressionExperiment()`
`ExpressionDataDoubleMatrix`	`getIntensity()`
`static ExpressionDataMatrix<?>`	`getMatrix(Collection<? extends DesignElementDataVector> vectors)` Create a matrix using all the vectors, which are assumed to all be of the same quantitation type.
`ExpressionDataBooleanMatrix`	`getMissingValueData()`
`static Collection<QuantitationType>`	`getMissingValueQuantitationTypes(ExpressionExperiment expressionExperiment)`
`Integer`	`getNumMissingValues(QuantitationType qt)`
`static Collection<QuantitationType>`	`getPreferredAndMissingQuantitationTypes(ExpressionExperiment expressionExperiment)`
`ExpressionDataDoubleMatrix`	`getPreferredData()`
`List<QuantitationType>`	`getPreferredQTypes()`
`static Collection<QuantitationType>`	`getPreferredQuantitationTypes(ExpressionExperiment expressionExperiment)`
`ExpressionDataDoubleMatrix`	`getProcessedData()`
`Map<CompositeSequence,Double>`	`getRanksByMean()`
`ExpressionDataDoubleMatrix`	`getSignalChannelA()`
`ExpressionDataDoubleMatrix`	`getSignalChannelB()`
`static Collection<QuantitationType>`	`getUsefulQuantitationTypes(Collection<QuantitationType> eeQtTypes)`
`static Collection<QuantitationType>`	`getUsefulQuantitationTypes(ExpressionExperiment expressionExperiment)`
`boolean`	`isAnyMissing()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - ExpressionDataMatrixBuilder
```
public ExpressionDataMatrixBuilder(Collection<? extends DesignElementDataVector> vectors)
```
    Parameters:
    
    vectors - collection of vectors. They should be thawed first.
  - ExpressionDataMatrixBuilder
```
public ExpressionDataMatrixBuilder(Collection<ProcessedExpressionDataVector> processedVectors,
                                   Collection<? extends DesignElementDataVector> otherVectors)
```
- Method Detail
  - getMatrix
```
public static ExpressionDataMatrix<?> getMatrix(Collection<? extends DesignElementDataVector> vectors)
```
    Create a matrix using all the vectors, which are assumed to all be of the same quantitation type.
    
    Parameters:
    
    vectors - raw vectors
    
    Returns:
    
    matrix of appropriate type.
  - getMissingValueQuantitationTypes
```
public static Collection<QuantitationType> getMissingValueQuantitationTypes(ExpressionExperiment expressionExperiment)
```
    Parameters:
    
    expressionExperiment - (should be lightly thawed)
    
    Returns:
    
    a collection of QTs
  - getPreferredAndMissingQuantitationTypes
```
public static Collection<QuantitationType> getPreferredAndMissingQuantitationTypes(ExpressionExperiment expressionExperiment)
```
  - getPreferredQuantitationTypes
```
public static Collection<QuantitationType> getPreferredQuantitationTypes(ExpressionExperiment expressionExperiment)
```
  - getUsefulQuantitationTypes
```
public static Collection<QuantitationType> getUsefulQuantitationTypes(Collection<QuantitationType> eeQtTypes)
```
    Parameters:
    
    eeQtTypes - the QTs
    
    Returns:
    
    just the quantitation types that are likely to be 'useful': Preferred, present/absent, signals and background from both channels (if present).
  - getUsefulQuantitationTypes
```
public static Collection<QuantitationType> getUsefulQuantitationTypes(ExpressionExperiment expressionExperiment)
```
    Parameters:
    
    expressionExperiment - the EE to get the QTs for
    
    Returns:
    
    just the quantitation types that are likely to be 'useful': Preferred, present/absent, signals and background from both channels (if present).
  - getBackgroundChannelA
```
public ExpressionDataDoubleMatrix getBackgroundChannelA()
```
  - getBackgroundChannelB
```
public ExpressionDataDoubleMatrix getBackgroundChannelB()
```
  - getBioAssayDimensions
```
public List<BioAssayDimension> getBioAssayDimensions()
```
    Returns:
    
    a single BioAssayDimension except if there are multiple array designs used in the experiment.
  - getBkgSubChannelA
```
public ExpressionDataDoubleMatrix getBkgSubChannelA()
```
  - getExpressionExperiment
```
public ExpressionExperiment getExpressionExperiment()
```
  - getIntensity
```
public ExpressionDataDoubleMatrix getIntensity()
```
    Returns:
    
    Compute an intensity matrix. For two-channel arrays, this is the geometric mean of the background-subtracted signals on the two channels. For two-color arrays, if one channel is missing (as happens sometimes) the intensities returned are just from the one channel. For one-color arrays, this is the same as the preferred data matrix.
  - getMissingValueData
```
public ExpressionDataBooleanMatrix getMissingValueData()
```
    Returns:
    
    a matrix of booleans, or null if a missing value quantitation type ("absent/present", which may have been computed by our system) is not found. This will return the values whether the array design is two-color or not.
  - getNumMissingValues
```
public Integer getNumMissingValues(QuantitationType qt)
```
  - getPreferredData
```
public ExpressionDataDoubleMatrix getPreferredData()
```
    Returns:
    
    The matrix for the preferred data - NOT the processed data (though they may be the same, in fact)
  - getPreferredQTypes
```
public List<QuantitationType> getPreferredQTypes()
```
  - getProcessedData
```
public ExpressionDataDoubleMatrix getProcessedData()
```
  - getRanksByMean
```
public Map<CompositeSequence,Double> getRanksByMean()
```
  - getSignalChannelA
```
public ExpressionDataDoubleMatrix getSignalChannelA()
```
  - getSignalChannelB
```
public ExpressionDataDoubleMatrix getSignalChannelB()
```
  - isAnyMissing
```
public boolean isAnyMissing()
```

Class ExpressionDataMatrixBuilder

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ExpressionDataMatrixBuilder

ExpressionDataMatrixBuilder

Method Detail

getMatrix

getMissingValueQuantitationTypes

getPreferredAndMissingQuantitationTypes

getPreferredQuantitationTypes

getUsefulQuantitationTypes

getUsefulQuantitationTypes

getBackgroundChannelA

getBackgroundChannelB

getBioAssayDimensions

getBkgSubChannelA

getExpressionExperiment

getIntensity

getMissingValueData

getNumMissingValues

getPreferredData

getPreferredQTypes

getProcessedData

getRanksByMean

getSignalChannelA

getSignalChannelB

isAnyMissing