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

Class ComBat<R,C>

java.lang.Object

ubic.gemma.core.analysis.preprocess.batcheffects.ComBat<R,C>

public class ComBat<R,C>
extends Object

An implementation of the ComBat algorithm described by Johson et al as described in:

Johnson, WE, Rabinovic, A, and Li, C (2007). Adjusting batch effects in microarray expression data using Empirical Bayes methods. Biostatistics 8(1):118-127.

Constructor Summary

Constructors

Constructor	Description
ComBat(DoubleMatrix<R,C> data, ObjectMatrix<C,String,?> sampleInfo)
ComBat(ObjectMatrix<C,String,?> sampleInfo)	Constructor that can be used just for testing correctability (data is not provided) - FIXME refactor so it's not a constructor.

Method Summary

Modifier and Type	Method	Description
DoubleMatrix2D	getDesignMatrix()
void	plot(String filePrefix)	Make diagnostic plots.
DoubleMatrix2D	run()
DoubleMatrix2D	run(boolean parametric)

Methods inherited from class java.lang.Object

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

Constructor Detail

ComBat

public ComBat(ObjectMatrix<C,String,?> sampleInfo)
       throws ubic.gemma.core.analysis.preprocess.batcheffects.ComBatException

Constructor that can be used just for testing correctability (data is not provided) - FIXME refactor so it's not a constructor.

Parameters:

sampleInfo -

Throws:

ubic.gemma.core.analysis.preprocess.batcheffects.ComBatException

ComBat

public ComBat(DoubleMatrix<R,C> data,
              ObjectMatrix<C,String,?> sampleInfo)
       throws ubic.gemma.core.analysis.preprocess.batcheffects.ComBatException

Throws:

ubic.gemma.core.analysis.preprocess.batcheffects.ComBatException

Method Detail

getDesignMatrix

public DoubleMatrix2D getDesignMatrix()

plot

public void plot(String filePrefix)

Make diagnostic plots. FIXME: As in the original ComBat, this only graphs the first batch's statistics. In principle we can (and perhaps should) examine these plots for all the batches.

Parameters:

filePrefix - file prefix

run

public DoubleMatrix2D run()
                   throws ubic.gemma.core.analysis.preprocess.batcheffects.ComBatException

Returns:

data corrected using parametric prior estimator

Throws:

ubic.gemma.core.analysis.preprocess.batcheffects.ComBatException - combat problems

run

public DoubleMatrix2D run(boolean parametric)
                   throws ubic.gemma.core.analysis.preprocess.batcheffects.ComBatException

Parameters:

parametric - if false, use the non-parametric (slower) method for estimating the priors.

Returns:

corrected data

Throws:

ubic.gemma.core.analysis.preprocess.batcheffects.ComBatException - combat problems