ComBat (Gemma 1.30.3 API)

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)

Method Summary

All Methods Instance Methods Concrete Methods
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(DoubleMatrix<R,C> data,
              ObjectMatrix<C,String,?> sampleInfo)
```
- 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