Examples with ExpressionAnalysisResultSet ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet used on opensource projects

Example 21 with ExpressionAnalysisResultSet

use of ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet in project Gemma by PavlidisLab.

the class DifferentialExpressionAnalyzerServiceTest method testAnalyzeAndDelete.

@Test
public void testAnalyzeAndDelete() throws Exception {
    assert ee.getId() != null;
    DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig();
    Collection<ExperimentalFactor> factors = ee.getExperimentalDesign().getExperimentalFactors();
    config.setFactorsToInclude(factors);
    config.addInteractionToInclude(factors);
    Collection<DifferentialExpressionAnalysis> analyses = differentialExpressionAnalyzerService.runDifferentialExpressionAnalyses(ee, config);
    assertNotNull(analyses);
    assertTrue(!analyses.isEmpty());
    assertNotNull(analyses.iterator().next());
    DifferentialExpressionAnalysis analysis = differentialExpressionAnalysisService.thawFully(analyses.iterator().next());
    aclTestUtils.checkHasAcl(analysis);
    aclTestUtils.checkLacksAces(analysis);
    aclTestUtils.checkHasAclParent(analysis, ee);
    for (ExpressionAnalysisResultSet rs : analysis.getResultSets()) {
        assertTrue(!rs.getResults().isEmpty());
        assertEquals(99, rs.getResults().size());
    }
    // avoid adding annotations for genes, it confuses the reader.
    for (ArrayDesign ad : expressionExperimentService.getArrayDesignsUsed(ee)) {
        this.arrayDesignAnnotationService.deleteExistingFiles(ad);
    }
    Collection<File> outputLocations = expressionDataFileService.writeOrLocateDiffExpressionDataFiles(ee, true);
    assertEquals(1, outputLocations.size());
    File outputLocation = outputLocations.iterator().next();
    // NOte that this reader generally won't work for experiment files because of the gene annotations.
    DoubleMatrixReader r = new DoubleMatrixReader();
    assertTrue(outputLocation.canRead());
    DoubleMatrix<String, String> readIn = r.read(outputLocation.getAbsolutePath());
    assertEquals(99, readIn.rows());
    System.out.println(readIn.toString());
    assertEquals(9, readIn.columns());
    expressionDataFileService.deleteAllFiles(ee);
    // / remove the analysis
    int numDeleted = differentialExpressionAnalyzerService.deleteAnalyses(ee);
    assertTrue(numDeleted > 0);
}

Example 22 with ExpressionAnalysisResultSet

use of ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet in project Gemma by PavlidisLab.

the class DifferentialExpressionAnalyzerServiceTest method testWritePValuesHistogram.

@Test
public void testWritePValuesHistogram() {
    DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig();
    Collection<ExperimentalFactor> factors = ee.getExperimentalDesign().getExperimentalFactors();
    config.setFactorsToInclude(factors);
    Collection<DifferentialExpressionAnalysis> analyses = differentialExpressionAnalyzerService.runDifferentialExpressionAnalyses(ee, config);
    for (DifferentialExpressionAnalysis analysis : analyses) {
        differentialExpressionAnalysisService.thaw(analysis);
        for (ExpressionAnalysisResultSet resultSet : analysis.getResultSets()) {
            Histogram hist = resultService.loadPvalueDistribution(resultSet.getId());
            assertNotNull(hist);
        }
    }
}

Example 23 with ExpressionAnalysisResultSet

use of ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet in project Gemma by PavlidisLab.

the class SubsettedAnalysisTest method testWithSubset.

@Test
public final void testWithSubset() {
    this.configureMocks();
    DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig();
    config.getFactorsToInclude().add(this.experimentalFactorA_Area);
    config.setSubsetFactor(this.experimentalFactorB);
    Collection<DifferentialExpressionAnalysis> expressionAnalyses = analyzer.run(expressionExperiment, config);
    assertEquals(2, expressionAnalyses.size());
    for (DifferentialExpressionAnalysis expressionAnalysis : expressionAnalyses) {
        assertNotNull(expressionAnalysis.getExperimentAnalyzed());
        assertEquals(4, expressionAnalysis.getExperimentAnalyzed().getBioAssays().size());
        Collection<ExpressionAnalysisResultSet> resultSets = expressionAnalysis.getResultSets();
        ExpressionAnalysisResultSet resultSet = resultSets.iterator().next();
        int numResults = resultSet.getResults().size();
        // we should have filtered some out.
        assertTrue(numResults < 100);
    }
}

Example 24 with ExpressionAnalysisResultSet

use of ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet in project Gemma by PavlidisLab.

the class DiffExTest method testGSE35930.

/**
 * Test where probes have constant values. See bug 3177.
 */
@Test
public void testGSE35930() throws Exception {
    ExpressionExperiment ee;
    // eeService.remove( eeService.findByShortName( "GSE35930" ) );
    try {
        geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath("GSE35930")));
        Collection<?> results = geoService.fetchAndLoad("GSE35930", false, true, false);
        ee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        // OK.
        if (e.getData() instanceof List) {
            ee = (ExpressionExperiment) ((List<?>) e.getData()).iterator().next();
        } else {
            ee = (ExpressionExperiment) e.getData();
        }
    }
    ee = this.eeService.thawLite(ee);
    processedExpressionDataVectorService.computeProcessedExpressionData(ee);
    if (ee.getExperimentalDesign().getExperimentalFactors().isEmpty()) {
        ee = eeService.load(ee.getId());
        ee = this.eeService.thawLite(ee);
        try (InputStream is = this.getClass().getResourceAsStream("/data/loader/expression/geo/GSE35930/design.txt")) {
            experimentalDesignImporter.importDesign(ee, is);
        }
        ee = eeService.load(ee.getId());
        ee = this.eeService.thawLite(ee);
    }
    DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig();
    config.setFactorsToInclude(ee.getExperimentalDesign().getExperimentalFactors());
    Collection<DifferentialExpressionAnalysis> analyses = analyzer.run(ee, config);
    assertNotNull(analyses);
    assertEquals(1, analyses.size());
    DifferentialExpressionAnalysis results = analyses.iterator().next();
    boolean found = false;
    ExpressionAnalysisResultSet resultSet = results.getResultSets().iterator().next();
    for (DifferentialExpressionAnalysisResult r : resultSet.getResults()) {
        // this probe has a constant value
        if (r.getProbe().getName().equals("1622910_at")) {
            fail("Should not have found a result for constant probe");
        // found = true;
        // assertTrue( "Got: " + pvalue, pvalue == null || pvalue.equals( Double.NaN ) );
        } else {
            // got to have something...
            found = true;
        }
    }
    assertTrue(found);
}

Example 25 with ExpressionAnalysisResultSet

use of ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet in project Gemma by PavlidisLab.

the class DiffExTest method testCountData.

/**
 * Test differential expression analysis on RNA-seq data. See bug 3383. R code in voomtest.R
 */
@Test
public void testCountData() throws Exception {
    geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGenerator());
    ExpressionExperiment ee = eeService.findByShortName("GSE29006");
    if (ee != null) {
        eeService.remove(ee);
    }
    assertTrue(eeService.findByShortName("GSE29006") == null);
    try {
        Collection<?> results = geoService.fetchAndLoad("GSE29006", false, false, false);
        ee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        throw new IllegalStateException("Need to remove this data set before test is run");
    }
    ee = eeService.thaw(ee);
    try (InputStream is = this.getClass().getResourceAsStream("/data/loader/expression/flatfileload/GSE29006_design.txt")) {
        assertNotNull(is);
        experimentalDesignImporter.importDesign(ee, is);
    }
    // Load the data from a text file.
    DoubleMatrixReader reader = new DoubleMatrixReader();
    ArrayDesign targetArrayDesign;
    try (InputStream countData = this.getClass().getResourceAsStream("/data/loader/expression/flatfileload/GSE29006_expression_count.test.txt")) {
        DoubleMatrix<String, String> countMatrix = reader.read(countData);
        Collection<ExperimentalFactor> experimentalFactors = ee.getExperimentalDesign().getExperimentalFactors();
        assertEquals(1, experimentalFactors.size());
        List<String> probeNames = countMatrix.getRowNames();
        assertEquals(199, probeNames.size());
        // we have to find the right generic platform to use.
        targetArrayDesign = this.getTestPersistentArrayDesign(probeNames, taxonService.findByCommonName("human"));
        targetArrayDesign = arrayDesignService.thaw(targetArrayDesign);
        // the experiment has 8 samples but the data has 4 columns so allow missing samples
        // GSM718707 GSM718708 GSM718709 GSM718710
        dataUpdater.addCountData(ee, targetArrayDesign, countMatrix, null, 36, true, true);
    }
    // make sure to do a thawRawAndProcessed() to get the addCountData() updates
    ee = eeService.thaw(ee);
    // verify rows and columns
    Collection<DoubleVectorValueObject> processedDataArrays = processedExpressionDataVectorService.getProcessedDataArrays(ee);
    assertEquals(199, processedDataArrays.size());
    for (DoubleVectorValueObject v : processedDataArrays) {
        assertEquals(4, v.getBioAssays().size());
    }
    // I confirmed that log2cpm is working same as voom here; not bothering to test directly.
    TestUtils.assertBAs(ee, targetArrayDesign, "GSM718709", 320383);
    // DE analysis without weights to assist comparison to R
    DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig();
    config.setUseWeights(false);
    config.setFactorsToInclude(ee.getExperimentalDesign().getExperimentalFactors());
    Collection<DifferentialExpressionAnalysis> analyses = analyzer.run(ee, config);
    assertNotNull(analyses);
    assertEquals(1, analyses.size());
    DifferentialExpressionAnalysis results = analyses.iterator().next();
    boolean found = false;
    ExpressionAnalysisResultSet resultSet = results.getResultSets().iterator().next();
    for (DifferentialExpressionAnalysisResult r : resultSet.getResults()) {
        if (r.getProbe().getName().equals("ENSG00000000938")) {
            found = true;
            ContrastResult contrast = r.getContrasts().iterator().next();
            assertEquals(0.007055717, r.getPvalue(), // R: 0.006190738; coeff = 2.2695215; t=12.650422; R with our weights: 0.009858270, 2.2317534; t=9.997007
            0.00001);
            // up to sign
            assertEquals(2.2300049, Math.abs(contrast.getCoefficient()), 0.001);
            break;
        }
    }
    assertTrue(found);
    // With weights
    config = new DifferentialExpressionAnalysisConfig();
    // <----
    config.setUseWeights(true);
    config.setFactorsToInclude(ee.getExperimentalDesign().getExperimentalFactors());
    analyses = analyzer.run(ee, config);
    results = analyses.iterator().next();
    resultSet = results.getResultSets().iterator().next();
    for (DifferentialExpressionAnalysisResult r : resultSet.getResults()) {
        if (r.getProbe().getName().equals("ENSG00000000938")) {
            assertEquals(1, r.getContrasts().size());
            ContrastResult contrast = r.getContrasts().iterator().next();
            // yes!
            assertEquals(2.232816, Math.abs(contrast.getCoefficient()), 0.001);
            assertEquals(0.000311, contrast.getPvalue(), 0.00001);
            assertEquals(56.66342, Math.abs(contrast.getTstat()), 0.001);
            assertEquals(0.007068, r.getPvalue(), 0.00001);
            break;
        }
    }
}