Examples with GeoSeries ubic.gemma.core.loader.expression.geo.model.GeoSeries used on opensource projects

Example 36 with GeoSeries

use of ubic.gemma.core.loader.expression.geo.model.GeoSeries in project Gemma by PavlidisLab.

the class TwoChannelMissingValuesTest method testMissingValueGSE11017.

/**
 * Was giving all missing values.
 */
@Test
public void testMissingValueGSE11017() throws Exception {
    ExpressionExperiment old = eeService.findByShortName("GSE11017");
    if (old != null)
        eeService.remove(old);
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GSE11017.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE11017");
    DatasetCombiner datasetCombiner = new DatasetCombiner();
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    Object result = this.gc.convert(series);
    assertNotNull(result);
    ExpressionExperiment expExp = (ExpressionExperiment) ((Collection<?>) result).iterator().next();
    expExp = persisterHelper.persist(expExp, persisterHelper.prepare(expExp));
    Collection<RawExpressionDataVector> calls = tcmv.computeMissingValues(expExp, 2.0, new ArrayList<Double>());
    // print( calls );
    assertEquals(20, calls.size());
    boolean hasNewQT = false;
    Collection<QuantitationType> qts = eeService.getQuantitationTypes(expExp);
    for (QuantitationType qt : qts) {
        if (qt.getType().equals(StandardQuantitationType.PRESENTABSENT)) {
            hasNewQT = true;
            break;
        }
    }
    assertTrue(hasNewQT);
    ExpressionDataMatrixBuilder builder = new ExpressionDataMatrixBuilder(calls);
    ExpressionDataBooleanMatrix missingValues = builder.getMissingValueData();
    assertTrue(missingValues.getQuantitationTypes().iterator().next().getDescription().contains("signal threshold"));
    Boolean[][] mm = missingValues.getRawMatrix();
    boolean hasPresent = false;
    for (Boolean[] aMm : mm) {
        for (Boolean anAMm : aMm) {
            if (anAMm) {
                hasPresent = true;
                break;
            }
        }
    }
    assertTrue(hasPresent);
}

Example 37 with GeoSeries

use of ubic.gemma.core.loader.expression.geo.model.GeoSeries in project Gemma by PavlidisLab.

the class TwoChannelMissingValuesTest method testMissingValueGSE523.

@Test
public final void testMissingValueGSE523() throws Exception {
    ExpressionExperiment old = eeService.findByShortName("GSE523");
    if (old != null)
        eeService.remove(old);
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GSE523_family.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE523");
    DatasetCombiner datasetCombiner = new DatasetCombiner();
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    Object result = this.gc.convert(series);
    assertNotNull(result);
    ExpressionExperiment expExp = (ExpressionExperiment) ((Collection<?>) result).iterator().next();
    expExp = persisterHelper.persist(expExp, persisterHelper.prepare(expExp));
    Collection<RawExpressionDataVector> calls = tcmv.computeMissingValues(expExp, 2.0, new ArrayList<Double>());
    assertEquals(30, calls.size());
}

Example 38 with GeoSeries

use of ubic.gemma.core.loader.expression.geo.model.GeoSeries 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);
}