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

Example 16 with DifferentialExpressionAnalysisResult

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

the class SubsettedAnalysis3Test method test.

@Test
public void test() {
    ee = expressionExperimentService.thawLite(ee);
    Collection<ExperimentalFactor> factors = ee.getExperimentalDesign().getExperimentalFactors();
    assertEquals(3, factors.size());
    for (BioAssay ba : ee.getBioAssays()) {
        assertEquals(3, ba.getSampleUsed().getFactorValues().size());
    }
    ExperimentalFactor organismpart = null;
    ExperimentalFactor disease = null;
    ExperimentalFactor diseasegroup = null;
    for (ExperimentalFactor ef : factors) {
        switch(ef.getCategory().getValue()) {
            case "study design":
                diseasegroup = ef;
                break;
            case "disease":
                disease = ef;
                break;
            case "organism part":
                organismpart = ef;
                break;
        }
    }
    assertNotNull(diseasegroup);
    assertNotNull(disease);
    assertNotNull(organismpart);
    DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig();
    config.getFactorsToInclude().add(disease);
    config.getFactorsToInclude().add(organismpart);
    config.setSubsetFactor(diseasegroup);
    Collection<DifferentialExpressionAnalysis> analyses = analyzer.run(ee, config);
    // a subset for each disease: SZ, PD, HD, ALS, ALZ, MS
    assertEquals(6, analyses.size());
    /*
         * Now, within each we should have only one disease contrast,
         */
    for (DifferentialExpressionAnalysis analysis : analyses) {
        // there should be one for disease - tissue isn't used.
        assertEquals(1, analysis.getResultSets().size());
        for (ExpressionAnalysisResultSet rs : analysis.getResultSets()) {
            ExperimentalFactor factor = rs.getExperimentalFactors().iterator().next();
            // noinspection LoopStatementThatDoesntLoop
            for (DifferentialExpressionAnalysisResult res : rs.getResults()) {
                Collection<ContrastResult> contrasts = res.getContrasts();
                for (ContrastResult cr : contrasts) {
                    log.info(analysis + "   " + factor + " " + cr + " " + res);
                }
                break;
            }
        }
    }
}

Example 17 with DifferentialExpressionAnalysisResult

use of ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult 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 18 with DifferentialExpressionAnalysisResult

use of ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult 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;
        }
    }
}

Example 19 with DifferentialExpressionAnalysisResult

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

the class AncovaTest method testAncovaContinuousCovariate.

/*
     * With a continuous covariate only
     */
@Test
public void testAncovaContinuousCovariate() {
    this.configureMocks();
    /*
         * Add a continuous factor
         */
    ExperimentalFactor experimentalFactorC = ExperimentalFactor.Factory.newInstance();
    experimentalFactorC.setName("confabulatiliationity");
    experimentalFactorC.setId(5399424551L);
    experimentalFactorC.setType(FactorType.CONTINUOUS);
    this.setupFactorValues(experimentalFactorC);
    // leave off the others.
    expressionExperiment.getExperimentalDesign().getExperimentalFactors().clear();
    expressionExperiment.getExperimentalDesign().getExperimentalFactors().add(experimentalFactorC);
    DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig();
    config.setFactorsToInclude(expressionExperiment.getExperimentalDesign().getExperimentalFactors());
    Collection<DifferentialExpressionAnalysis> expressionAnalyses = analyzer.run(expressionExperiment, config);
    assertTrue(!expressionAnalyses.isEmpty());
    DifferentialExpressionAnalysis expressionAnalysis = expressionAnalyses.iterator().next();
    assertNotNull(expressionAnalysis);
    Collection<ExpressionAnalysisResultSet> resultSets = expressionAnalysis.getResultSets();
    assertEquals(1, resultSets.size());
    for (ExpressionAnalysisResultSet resultSet : resultSets) {
        Collection<ExperimentalFactor> factors = resultSet.getExperimentalFactors();
        assertEquals(1, factors.size());
        assertEquals(100, resultSet.getResults().size());
        for (DifferentialExpressionAnalysisResult r : resultSet.getResults()) {
            assertNotNull(r.getCorrectedPvalue());
        }
    }
}

Example 20 with DifferentialExpressionAnalysisResult

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

the class DifferentialExpressionAnalyzerServiceImpl method persistAnalysis.

/**
 * Made public for testing purposes only.
 *
 * @param config               config
 * @param analysis             analysis
 * @param expressionExperiment the experiment
 * @return DEA
 */
@Override
public DifferentialExpressionAnalysis persistAnalysis(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysis analysis, DifferentialExpressionAnalysisConfig config) {
    this.deleteOldAnalyses(expressionExperiment, analysis, config.getFactorsToInclude());
    StopWatch timer = new StopWatch();
    timer.start();
    Collection<ExpressionAnalysisResultSet> resultSets = analysis.getResultSets();
    analysis.setResultSets(new HashSet<ExpressionAnalysisResultSet>());
    // first transaction, gets us an ID
    DifferentialExpressionAnalysis persistentAnalysis = helperService.persistStub(analysis);
    // second set of transactions creates the empty resultSets.
    for (ExpressionAnalysisResultSet rs : resultSets) {
        Collection<DifferentialExpressionAnalysisResult> results = rs.getResults();
        rs.setResults(new HashSet<DifferentialExpressionAnalysisResult>());
        ExpressionAnalysisResultSet prs = helperService.create(rs);
        assert prs != null;
        for (DifferentialExpressionAnalysisResult r : results) {
            r.setResultSet(prs);
        }
        analysis.getResultSets().add(prs);
        rs.getResults().addAll(results);
        this.addPvalueDistribution(prs);
    }
    // third transaction - add results.
    DifferentialExpressionAnalyzerServiceImpl.log.info("Saving results");
    helperService.addResults(persistentAnalysis, resultSets);
    // get a clean copy of the analysis object from the DB.
    analysis = differentialExpressionAnalysisService.load(analysis.getId());
    // we do this here because now we have IDs for everything.
    try {
        expressionDataFileService.writeDiffExArchiveFile(expressionExperiment, analysis, config);
    } catch (IOException e) {
        DifferentialExpressionAnalyzerServiceImpl.log.error("Unable to save the data to a file: " + e.getMessage());
    }
    // final transaction: audit.
    try {
        auditTrailService.addUpdateEvent(expressionExperiment, DifferentialExpressionAnalysisEvent.Factory.newInstance(), persistentAnalysis.getDescription() + "; analysis id=" + persistentAnalysis.getId());
    } catch (Exception e) {
        DifferentialExpressionAnalyzerServiceImpl.log.error("Error while trying to add audit event: " + e.getMessage(), e);
        DifferentialExpressionAnalyzerServiceImpl.log.error("Continuing ...");
    /*
             * We shouldn't fail completely due to this.
             */
    }
    if (timer.getTime() > 5000) {
        DifferentialExpressionAnalyzerServiceImpl.log.info("Save results: " + timer.getTime() + "ms");
    }
    return persistentAnalysis;
}