Examples with ExpressionDataMatrixBuilder ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder used on opensource projects

Example 1 with ExpressionDataMatrixBuilder

use of ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder in project Gemma by PavlidisLab.

the class ExpressionDataDoubleMatrixTest method testMatrixConversion.

@Test
public void testMatrixConversion() throws Exception {
    try {
        geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath("")));
        Collection<?> results = geoService.fetchAndLoad("GSE8294", false, true, false);
        newee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        newee = (ExpressionExperiment) ((List<?>) e.getData()).iterator().next();
    }
    newee = expressionExperimentService.thaw(newee);
    // make sure we really thawRawAndProcessed them, so we can get the design element sequences.
    Collection<RawExpressionDataVector> vectors = newee.getRawExpressionDataVectors();
    rawExpressionDataVectorService.thaw(vectors);
    ExpressionDataMatrixBuilder builder = new ExpressionDataMatrixBuilder(vectors);
    ExpressionDataDoubleMatrix matrix = builder.getPreferredData();
    assertTrue(!Double.isNaN(matrix.get(10, 0)));
    assertEquals(66, matrix.rows());
    assertEquals(9, matrix.columns());
    /*
         * Additional tests for files and outlier marking.
         */
    processedDataVectorService.computeProcessedExpressionData(newee);
    File f1 = expressionDataFileService.writeOrLocateDataFile(expressionExperimentService.load(newee.getId()), true, true);
    assertNotNull(f1);
    assertTrue(f1.exists());
    expressionDataFileService.deleteAllFiles(newee);
    assertTrue(!f1.exists());
    /*
         * outlier removal.
         */
    BioAssay tba = newee.getBioAssays().iterator().next();
    Collection<BioAssay> ol = new HashSet<>();
    ol.add(tba);
    sampleRemoveService.markAsMissing(ol);
    assertTrue(tba.getIsOutlier());
    newee = expressionExperimentService.thaw(newee);
    Collection<ProcessedExpressionDataVector> vecs = newee.getProcessedExpressionDataVectors();
    this.processedDataVectorService.thaw(vecs);
    assertTrue(!vecs.isEmpty());
    ExpressionDataMatrixBuilder matrixBuilder = new ExpressionDataMatrixBuilder(vecs);
    ExpressionDataDoubleMatrix data = matrixBuilder.getProcessedData();
    assertNotNull(data);
    assertTrue(Double.isNaN(data.getColumn(tba)[10]));
    sampleRemoveService.unmarkAsMissing(ol);
    newee = expressionExperimentService.load(newee.getId());
    newee = expressionExperimentService.thaw(newee);
    vecs = newee.getProcessedExpressionDataVectors();
    this.processedDataVectorService.thaw(vecs);
    assertTrue(!vecs.isEmpty());
    matrixBuilder = new ExpressionDataMatrixBuilder(vecs);
    data = matrixBuilder.getProcessedData();
    assertTrue(!tba.getIsOutlier());
    assertTrue(!Double.isNaN(data.getColumn(tba)[10]));
}

Example 2 with ExpressionDataMatrixBuilder

use of ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder in project Gemma by PavlidisLab.

the class GeoDatasetServiceTest method testFetchAndLoadMultiChipPerSeriesShort.

@Test
public void testFetchAndLoadMultiChipPerSeriesShort() throws Exception {
    geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath("shortTest")));
    /*
         * HG-U133A. GDS473 is for the other chip (B). Series is GSE674. see
         * http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gds&term=GSE674[Accession]&cmd=search
         */
    ExpressionExperiment newee;
    try {
        Collection<?> results = geoService.fetchAndLoad("GSE674", false, true, false);
        newee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        log.info("Skipping test, data already exists in db");
        return;
    }
    assertNotNull(newee);
    newee = eeService.thaw(newee);
    /*
         * Test for bug 468 (merging of subsets across GDS's)
         */
    ExperimentalFactor factor = newee.getExperimentalDesign().getExperimentalFactors().iterator().next();
    // otherwise get 4.
    assertEquals(2, factor.getFactorValues().size());
    Collection<RawExpressionDataVector> vectors = newee.getRawExpressionDataVectors();
    rawExpressionDataVectorService.thaw(vectors);
    ExpressionDataMatrixBuilder builder = new ExpressionDataMatrixBuilder(vectors);
    ExpressionDataMatrix<Double> matrix = builder.getPreferredData();
    assertNotNull(matrix);
    assertEquals(31, matrix.rows());
    assertEquals(15, matrix.columns());
    // GSM10363 = D1-U133B
    this.testMatrixValue(newee, matrix, "200000_s_at", "GSM10363", 5722.0);
    // GSM10380 = C7-U133A
    this.testMatrixValue(newee, matrix, "1007_s_at", "GSM10380", 1272.0);
}