Package ubic.gemma.core.analysis.preprocess.batcheffects

Class ExpressionExperimentBatchCorrectionServiceImpl

java.lang.Object

ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImpl

All Implemented Interfaces:

ExpressionExperimentBatchCorrectionService

@Component
public class ExpressionExperimentBatchCorrectionServiceImpl
extends Object
implements ExpressionExperimentBatchCorrectionService

Methods for correcting batch effects.

Author:

paul

Field Summary

Fields

Modifier and Type	Field	Description
static final String	COLLECTION_OF_MATERIAL_URI
static final String	DE_EXCLUDE_URI
static final String	DE_INCLUDE_URI

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentBatchCorrectionServiceImpl()

Method Summary

Modifier and Type	Method	Description
boolean	checkCorrectability(ExpressionExperiment ee)	Is there a Batch factor provided? Is there a confound problem? Do we have at least two samples per batch? This will return true even if there is evidence the data has been batch-corrected before; we assume the caller wants to redo it based on the raw data
ExpressionDataDoubleMatrix	comBat(ExpressionExperiment ee)	Run ComBat using default settings (parametric)
ExpressionDataDoubleMatrix	comBat(ExpressionExperiment ee, ExpressionDataDoubleMatrix originalDataMatrix)	Run ComBat with a specific data matrix.
ExperimentalFactor	getBatchFactor(ExpressionExperiment ee)	For convenience of some testing classes
static ExpressionDataDoubleMatrix	removeOutliers(ExpressionDataDoubleMatrix originalDataMatrix, ExpressionExperiment ee)	Remove outlier samples from the data matrix, based on outliers that were flagged in the experiment (not just candidate outliers)

Methods inherited from class java.lang.Object

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

Field Details

COLLECTION_OF_MATERIAL_URI

public static final String COLLECTION_OF_MATERIAL_URI

See Also:

• Constant Field Values

DE_EXCLUDE_URI

public static final String DE_EXCLUDE_URI

See Also:

• Constant Field Values

DE_INCLUDE_URI

public static final String DE_INCLUDE_URI

See Also:

• Constant Field Values

Constructor Details

ExpressionExperimentBatchCorrectionServiceImpl

public ExpressionExperimentBatchCorrectionServiceImpl()

Method Details

checkCorrectability

public boolean checkCorrectability(ExpressionExperiment ee)

Description copied from interface: ExpressionExperimentBatchCorrectionService

Is there a Batch factor provided? Is there a confound problem? Do we have at least two samples per batch? This will return true even if there is evidence the data has been batch-corrected before; we assume the caller wants to redo it based on the raw data

Specified by:

checkCorrectability in interface ExpressionExperimentBatchCorrectionService

Parameters:

ee - the experiment

Returns:

whether it is correctable

comBat

public ExpressionDataDoubleMatrix comBat(ExpressionExperiment ee)

Description copied from interface: ExpressionExperimentBatchCorrectionService

Run ComBat using default settings (parametric)

The matrix is constructed from the experiment's processed vectors.

Specified by:

comBat in interface ExpressionExperimentBatchCorrectionService

comBat

public ExpressionDataDoubleMatrix comBat(ExpressionExperiment ee,
 ExpressionDataDoubleMatrix originalDataMatrix)

Description copied from interface: ExpressionExperimentBatchCorrectionService

Run ComBat with a specific data matrix.

Specified by:

comBat in interface ExpressionExperimentBatchCorrectionService

Parameters:

originalDataMatrix - the matrix

Returns:

batch corrected matrix, or null if there's no batching factor

removeOutliers

public static ExpressionDataDoubleMatrix removeOutliers(ExpressionDataDoubleMatrix originalDataMatrix,
 ExpressionExperiment ee)

Remove outlier samples from the data matrix, based on outliers that were flagged in the experiment (not just candidate outliers)

Returns:

the original matrix, or if outliers were present, a new matrix with the outliers removed

getBatchFactor

public ExperimentalFactor getBatchFactor(ExpressionExperiment ee)

Description copied from interface: ExpressionExperimentBatchCorrectionService

For convenience of some testing classes

Specified by:

getBatchFactor in interface ExpressionExperimentBatchCorrectionService

Parameters:

ee - the experiment to get the batch factor for

Returns:

the batch factor of the experiment, or null, if experiment has no batch factor