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

Interface ExpressionExperimentBatchCorrectionService

All Known Implementing Classes:

ExpressionExperimentBatchCorrectionServiceImpl

public interface ExpressionExperimentBatchCorrectionService

Author:

Paul

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(ExpressionDataDoubleMatrix mat)	Run ComBat using default settings (parametric)
ExpressionDataDoubleMatrix	comBat(ExpressionExperiment ee)
ExperimentalFactor	getBatchFactor(ExpressionExperiment ee)	For convenience of some testing classes

Method Detail

checkCorrectability

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

Parameters:

ee - the experiment

Returns:

whether it is correctable

comBat

@Nullable
ExpressionDataDoubleMatrix comBat(ExpressionDataDoubleMatrix mat)

Run ComBat using default settings (parametric)

Parameters:

mat - the matrix

Returns:

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

comBat

@Nullable
ExpressionDataDoubleMatrix comBat(ExpressionExperiment ee)

getBatchFactor

@Nullable
ExperimentalFactor getBatchFactor(ExpressionExperiment ee)

For convenience of some testing classes

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