Examples with ExpressionDataDoubleMatrix ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix used on opensource projects

Example 41 with ExpressionDataDoubleMatrix

use of ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix in project Gemma by PavlidisLab.

the class ExpressionDataSVDTest method testMatrixReconstructB.

/*
     * Test on full-sized data set.
     */
@Test
public void testMatrixReconstructB() throws Exception {
    GeoConverter gc = new GeoConverterImpl();
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/fullSizeTests/GSE1623_family.soft.txt.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE1623");
    DatasetCombiner datasetCombiner = new DatasetCombiner();
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    @SuppressWarnings("unchecked") Collection<ExpressionExperiment> result = (Collection<ExpressionExperiment>) gc.convert(series);
    assertNotNull(result);
    assertEquals(1, result.size());
    ExpressionExperiment ee = result.iterator().next();
    ExpressionDataDoubleMatrix matrix = new ExpressionDataDoubleMatrix(ee.getRawExpressionDataVectors(), ee.getQuantitationTypes().iterator().next());
    svd = new ExpressionDataSVD(matrix, false);
    ExpressionDataDoubleMatrix svdNormalize = svd.removeHighestComponents(1);
    assertNotNull(svdNormalize);
}