Examples with ExperimentalFactor ubic.gemma.model.expression.experiment.ExperimentalFactor used on opensource projects

Example 46 with ExperimentalFactor

use of ubic.gemma.model.expression.experiment.ExperimentalFactor 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 47 with ExperimentalFactor

use of ubic.gemma.model.expression.experiment.ExperimentalFactor in project Gemma by PavlidisLab.

the class SubsettedAnalysis3Test method setup.

@Before
public void setup() throws Exception {
    geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(FileTools.resourceToPath("/data/analysis/expression/gse26927short")));
    try {
        Collection<?> results = geoService.fetchAndLoad("GSE26927", false, true, false);
        ee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        ee = (ExpressionExperiment) ((Collection<?>) e.getData()).iterator().next();
    }
    ee = expressionExperimentService.thawLite(ee);
    Collection<ExperimentalFactor> toremove = new HashSet<>(ee.getExperimentalDesign().getExperimentalFactors());
    for (ExperimentalFactor ef : toremove) {
        experimentalFactorService.delete(ef);
        ee.getExperimentalDesign().getExperimentalFactors().remove(ef);
    }
    expressionExperimentService.update(ee);
    processedExpressionDataVectorService.computeProcessedExpressionData(ee);
    ee = expressionExperimentService.thaw(ee);
    designImporter.importDesign(ee, this.getClass().getResourceAsStream("/data/analysis/expression/gse26927short/2684_GSE26927_expdesign.data.txt"));
}

Example 48 with ExperimentalFactor

use of ubic.gemma.model.expression.experiment.ExperimentalFactor in project Gemma by PavlidisLab.

the class TTestAnalyzerTest method testTTestWithExpressionExperiment.

/**
 * Tests the t-test with an {@link ExpressionExperiment}.
 */
@Test
public void testTTestWithExpressionExperiment() {
    if (!connected) {
        log.warn("Could not establish R connection.  Skipping test ...");
        return;
    }
    this.configureMocks();
    Collection<ExperimentalFactor> factors = new HashSet<>();
    factors.add(super.experimentalFactorA_Area);
    DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig();
    config.setFactorsToInclude(factors);
    Collection<DifferentialExpressionAnalysis> expressionAnalyses = analyzer.run(expressionExperiment, config);
    DifferentialExpressionAnalysis expressionAnalysis = expressionAnalyses.iterator().next();
    Collection<ExpressionAnalysisResultSet> resultSets = expressionAnalysis.getResultSets();
    ExpressionAnalysisResultSet resultSet = resultSets.iterator().next();
    int numResults = resultSet.getResults().size();
    assertEquals(numResults, BaseAnalyzerConfigurationTest.NUM_DESIGN_ELEMENTS);
    assertEquals(factorValueA2, resultSet.getBaselineGroup());
    Collection<HitListSize> hitListSizes = resultSet.getHitListSizes();
    assertEquals(3 * 5, hitListSizes.size());
    // check
    for (DifferentialExpressionAnalysisResult r : resultSet.getResults()) {
        CompositeSequence probe = r.getProbe();
        Double pvalue = r.getPvalue();
        assertNotNull(pvalue);
        Collection<ContrastResult> contrasts = r.getContrasts();
        Double stat;
        if (contrasts.isEmpty()) {
            continue;
        }
        stat = contrasts.iterator().next().getTstat();
        log.debug("probe: " + probe + "; p-value: " + pvalue);
        switch(probe.getName()) {
            case "probe_0":
                assertEquals(1.48e-13, pvalue, 1e-15);
                assertNotNull(stat);
                assertEquals(-277.4, stat, 0.1);
                break;
            case "probe_4":
                assertEquals(0.0001523, pvalue, 0.000001);
                break;
            case "probe_17":
                assertEquals(8.832e-12, pvalue, 1e-15);
                break;
            case "probe_75":
                assertEquals(0.2483, pvalue, 0.001);
                break;
        }
    }
}

Example 49 with ExperimentalFactor

use of ubic.gemma.model.expression.experiment.ExperimentalFactor in project Gemma by PavlidisLab.

the class TTestAnalyzerTest method testOneSampleTtest.

@Test
public void testOneSampleTtest() throws Exception {
    if (!connected) {
        log.warn("Could not establish R connection.  Skipping test ...");
        return;
    }
    this.configureVectors(super.biomaterials, "/data/stat-tests/onesample-ttest-data.txt");
    this.configureMocks();
    Collection<ExperimentalFactor> factors = new HashSet<>();
    factors.add(super.experimentalFactorA_Area);
    /*
         * Remove factorValue from all the samples.
         */
    Iterator<FactorValue> iterator = experimentalFactorA_Area.getFactorValues().iterator();
    FactorValue toUse = iterator.next();
    FactorValue toRemove = iterator.next();
    experimentalFactorA_Area.getFactorValues().remove(toRemove);
    for (BioMaterial bm : super.biomaterials) {
        bm.getFactorValues().remove(toRemove);
        bm.getFactorValues().add(toUse);
    }
    // must be for one-sample to make sense.
    quantitationType.setIsRatio(true);
    quantitationType.setScale(ScaleType.LOG2);
    DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig();
    config.setFactorsToInclude(factors);
    Collection<DifferentialExpressionAnalysis> expressionAnalyses = analyzer.run(expressionExperiment, config);
    DifferentialExpressionAnalysis expressionAnalysis = expressionAnalyses.iterator().next();
    Collection<ExpressionAnalysisResultSet> resultSets = expressionAnalysis.getResultSets();
    ExpressionAnalysisResultSet resultSet = resultSets.iterator().next();
    assertEquals(null, resultSet.getBaselineGroup());
    int numResults = resultSet.getResults().size();
    assertEquals(BaseAnalyzerConfigurationTest.NUM_DESIGN_ELEMENTS - 4, numResults);
    // check
    for (DifferentialExpressionAnalysisResult r : resultSet.getResults()) {
        CompositeSequence probe = r.getProbe();
        Double pvalue = r.getPvalue();
        // Double stat = probeAnalysisResult.getEffectSize();
        log.debug("probe: " + probe + "; p-value: " + pvalue);
        assertNotNull(pvalue);
        switch(probe.getName()) {
            case "probe_0":
                assertEquals(0.03505, pvalue, 0.00001);
                break;
            case "probe_16":
                assertEquals(0.03476, pvalue, 0.0001);
                break;
            case "probe_17":
                assertEquals(0.03578, pvalue, 0.0001);
                break;
            case "probe_75":
                assertEquals(0.8897, pvalue, 0.0001);
                // assertEquals( -0.1507, stat, 0.0001 );
                break;
            case "probe_94":
                assertEquals(0.002717, pvalue, 0.0001);
                // assertEquals( 6.6087, stat, 0.001 );
                break;
        }
    }
}

Example 50 with ExperimentalFactor

use of ubic.gemma.model.expression.experiment.ExperimentalFactor in project Gemma by PavlidisLab.

the class CharacteristicServiceTest method setup.

@Before
public void setup() {
    ee = this.getTestPersistentBasicExpressionExperiment();
    ee.setCharacteristics(this.getTestPersistentCharacteristics(2));
    Characteristic[] eeChars = ee.getCharacteristics().toArray(new Characteristic[0]);
    eeChar1 = eeChars[0];
    eeChar2 = eeChars[1];
    eeService.update(ee);
    BioAssay ba = ee.getBioAssays().toArray(new BioAssay[0])[0];
    BioMaterial bm = ba.getSampleUsed();
    bm.setCharacteristics(this.getTestPersistentCharacteristics(1));
    bmService.update(bm);
    for (ExperimentalFactor ef : testHelper.getExperimentalFactors(ee.getExperimentalDesign())) {
        eeService.addFactor(ee, ef);
    }
    ExperimentalFactor ef = ee.getExperimentalDesign().getExperimentalFactors().iterator().next();
    for (FactorValue f : testHelper.getFactorValues(ef)) {
        eeService.addFactorValue(ee, f);
    }
    FactorValue fv = ef.getFactorValues().iterator().next();
    fv.setCharacteristics(this.getTestPersistentCharacteristics(1));
    fvService.update(fv);
}