Package ubic.gemma.core.analysis.preprocess.normalize

Class QuantileNormalizer<R,C>

java.lang.Object

ubic.gemma.core.analysis.preprocess.normalize.QuantileNormalizer<R,C>

public class QuantileNormalizer<R,C>
extends Object

Perform quantile normalization on a matrix, as described in:

Bolstad, B (2001) _Probe Level Quantile Normalization of High Density Oligonucleotide Array Data_. Unpublished manuscript PDF

Bolstad, B. M., Irizarry R. A., Astrand, M, and Speed, T. P. (2003) _A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance._ Bioinformatics 19(2) ,pp 185-193. web page. However, note that this deals with missing values differently than the Bioconductor implementation.

Author:

pavlidis

See Also:

• MatrixNormalizer

Constructor Summary

Constructors

Constructor	Description
QuantileNormalizer()

Method Summary

Modifier and Type	Method	Description
DoubleMatrix<R,C>	normalize(DoubleMatrix<R,C> dataMatrix)

Methods inherited from class java.lang.Object

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

Constructor Details

QuantileNormalizer

public QuantileNormalizer()

Method Details

normalize

public DoubleMatrix<R,C> normalize(DoubleMatrix<R,C> dataMatrix)