ubic.gemma.analysis.preprocess.normalize.ExpressionDataQuantileNormalizer.java Source code

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Here is the source code for ubic.gemma.analysis.preprocess.normalize.ExpressionDataQuantileNormalizer.java

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/*
 * The Gemma project
 * 
 * Copyright (c) 2008 University of British Columbia
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *       http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *
 */
package ubic.gemma.analysis.preprocess.normalize;

import org.apache.commons.lang.ArrayUtils;

import ubic.basecode.dataStructure.matrix.DoubleMatrix;
import ubic.gemma.datastructure.matrix.ExpressionDataDoubleMatrix;
import ubic.gemma.model.expression.biomaterial.BioMaterial;
import ubic.gemma.model.expression.designElement.CompositeSequence;

/**
 * @author Paul
 * @version $Id: ExpressionDataQuantileNormalizer.java,v 1.3 2011/11/05 21:37:41 paul Exp $
 */
public class ExpressionDataQuantileNormalizer {

    /**
     * Quantile normalize the matrix (in place)
     * 
     * @param matrix
     */
    public static void normalize(ExpressionDataDoubleMatrix matrix) {

        DoubleMatrix<CompositeSequence, BioMaterial> rawMatrix = matrix.getMatrix();

        QuantileNormalizer<CompositeSequence, BioMaterial> normalizer = new QuantileNormalizer<CompositeSequence, BioMaterial>();
        DoubleMatrix<CompositeSequence, BioMaterial> normalized = normalizer.normalize(rawMatrix);

        for (int i = 0; i < normalized.rows(); i++) {
            matrix.setRow(i, ArrayUtils.toObject(normalized.getRow(i)));
        }

    }
}