populate value of meanVariance

Author: ppavlidis

src/ubic/basecode/math/linearmodels/MeanVarianceEstimator.java

@@ -24,10 +24,6 @@
 
 import java.util.List;
 
-import org.apache.commons.math3.analysis.interpolation.LinearInterpolator;
-import org.apache.commons.math3.analysis.polynomials.PolynomialSplineFunction;
-import org.apache.commons.math3.exception.OutOfRangeException;
-
 import cern.colt.function.IntIntDoubleFunction;
 import cern.colt.list.DoubleArrayList;
 import cern.colt.list.IntArrayList;
@@ -36,12 +32,9 @@
 import cern.colt.matrix.impl.DenseDoubleMatrix1D;
 import cern.colt.matrix.impl.DenseDoubleMatrix2D;
 import cern.colt.matrix.linalg.Algebra;
-import cern.jet.stat.Descriptive;
-import ubic.basecode.dataStructure.matrix.DenseDoubleMatrix;
 import ubic.basecode.dataStructure.matrix.DoubleMatrix;
 import ubic.basecode.math.DescriptiveWithMissing;
 import ubic.basecode.math.MatrixRowStats;
-import ubic.basecode.math.MatrixStats;
 import ubic.basecode.math.Smooth;
 import ubic.basecode.math.linalg.QRDecomposition;
 
@@ -226,6 +219,7 @@ private void voom(DoubleMatrix2D designMatrix) {
         voomXY.viewColumn(0).assign(sx);
         voomXY.viewColumn(1).assign(sy);
         DoubleMatrix2D fit = Smooth.loessFit(voomXY);
+        this.meanVariance = voomXY;
         this.loess = fit;
 
         // quarterroot fitted counts
@@ -255,7 +249,6 @@ private void voom(DoubleMatrix2D designMatrix) {
             fittedValues = solver.mult(coeff.viewDice(), A.viewDice());
         }
 
-
         // back-compute the values we want
         // fitted.cpm <- 2^fitted.values
         // fitted.count <- 1e-6 * t(t(fitted.cpm)*(lib.size+1))