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

Example 36 with DifferentialExpressionAnalysis

use of ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis 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 37 with DifferentialExpressionAnalysis

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

the class DifferentialExpressionAnalyzerServiceTest method testAnalyzeWithSubsetWhenOneIsNotUsableAndWithInteractionInTheOther.

/**
 * Test inspired by bug 2605
 */
@Test
public void testAnalyzeWithSubsetWhenOneIsNotUsableAndWithInteractionInTheOther() throws Exception {
    ee = expressionExperimentService.findByShortName("GSE32136");
    if (ee == null) {
        geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath()));
        Collection<?> results = geoService.fetchAndLoad("GSE32136", false, true, false);
        ee = (ExpressionExperiment) results.iterator().next();
    }
    processedDataVectorService.createProcessedDataVectors(ee);
    ee = expressionExperimentService.thawLite(ee);
    Collection<ExperimentalFactor> experimentalFactors = ee.getExperimentalDesign().getExperimentalFactors();
    for (ExperimentalFactor experimentalFactor : experimentalFactors) {
        experimentalFactorService.delete(experimentalFactor);
    }
    ee = expressionExperimentService.thawLite(ee);
    try (InputStream is = this.getClass().getResourceAsStream("/data/loader/expression/geo/GSE32136.design.txt")) {
        assertNotNull(is);
        experimentalDesignImporter.importDesign(ee, is);
    }
    experimentalFactors = ee.getExperimentalDesign().getExperimentalFactors();
    assertEquals(3, experimentalFactors.size());
    differentialExpressionAnalyzerService.deleteAnalyses(ee);
    // Done with setting it up.
    Collection<ExperimentalFactor> factors = new HashSet<>();
    ExperimentalFactor subsetFactor = null;
    for (ExperimentalFactor ef : experimentalFactors) {
        if (ef.getName().equals("PooledTreatment")) {
            subsetFactor = ef;
        } else {
            factors.add(ef);
        }
    }
    assertNotNull(subsetFactor);
    assertEquals(2, factors.size());
    DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig();
    config.setFactorsToInclude(factors);
    config.setSubsetFactor(subsetFactor);
    HashSet<Collection<ExperimentalFactor>> ifacts = new HashSet<>();
    ifacts.add(factors);
    config.setInteractionsToInclude(ifacts);
    Collection<DifferentialExpressionAnalysis> analyses = differentialExpressionAnalyzerService.runDifferentialExpressionAnalyses(ee, config);
    assertEquals("Should have quietly ignored one of the subsets that is not analyzable", 1, analyses.size());
    DifferentialExpressionAnalysis analysis = analyses.iterator().next();
    assertEquals("Subsetting was not done correctly", subsetFactor, analysis.getSubsetFactorValue().getExperimentalFactor());
    assertEquals("Interaction was not retained in the analyzed subset", 3, analysis.getResultSets().size());
    ExpressionExperimentSubSet eeset = (ExpressionExperimentSubSet) analysis.getExperimentAnalyzed();
    aclTestUtils.checkEESubSetAcls(eeset);
    aclTestUtils.checkHasAcl(analysis);
    aclTestUtils.checkLacksAces(eeset);
    aclTestUtils.checkLacksAces(analysis);
    // check that we read it back correctly.
    {
        Map<ExpressionExperimentDetailsValueObject, Collection<DifferentialExpressionAnalysisValueObject>> vos = differentialExpressionAnalysisService.getAnalysesByExperiment(Collections.singleton(ee.getId()));
        // it will retrieve the analysis of the subset.
        assertEquals(1, vos.size());
    }
    // retrieve the analysis of the subset directly.
    {
        Map<ExpressionExperimentDetailsValueObject, Collection<DifferentialExpressionAnalysisValueObject>> vos = differentialExpressionAnalysisService.getAnalysesByExperiment(Collections.singleton(eeset.getId()));
        assertEquals(1, vos.size());
        for (DifferentialExpressionAnalysisValueObject vo : vos.entrySet().iterator().next().getValue()) {
            assertNotNull(vo.getSubsetFactorValue());
        }
    }
}

Example 38 with DifferentialExpressionAnalysis

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

the class DifferentialExpressionAnalyzerServiceTest method testAnalyzeAndDeleteSpecificAnalysisWithSubset.

/**
 * Tests running with a subset factor, then deleting.
 */
@Test
public void testAnalyzeAndDeleteSpecificAnalysisWithSubset() {
    ExperimentalFactor[] factors = ee.getExperimentalDesign().getExperimentalFactors().toArray(new ExperimentalFactor[] {});
    List<ExperimentalFactor> factorsToUse = Collections.singletonList(factors[0]);
    ExperimentalFactor subsetFactor = factors[1];
    DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig();
    config.setFactorsToInclude(factorsToUse);
    config.setSubsetFactor(subsetFactor);
    Collection<DifferentialExpressionAnalysis> analyses = differentialExpressionAnalyzerService.runDifferentialExpressionAnalyses(ee, config);
    assertTrue(!analyses.isEmpty());
    differentialExpressionAnalyzerService.deleteAnalysis(ee, analyses.iterator().next());
}

Example 39 with DifferentialExpressionAnalysis

use of ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis 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 40 with DifferentialExpressionAnalysis

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

the class SubsettedAnalysis2Test method test.

@Test
public void test() {
    ee = expressionExperimentService.thawLite(ee);
    Collection<ExperimentalFactor> factors = ee.getExperimentalDesign().getExperimentalFactors();
    // includes batch
    assertEquals(4, factors.size());
    for (BioAssay ba : ee.getBioAssays()) {
        assertEquals(4, ba.getSampleUsed().getFactorValues().size());
    }
    ExperimentalFactor strainOrLine = null;
    ExperimentalFactor genotype = null;
    ExperimentalFactor phenotype = null;
    for (ExperimentalFactor ef : factors) {
        switch(ef.getCategory().getValue()) {
            case "genotype":
                genotype = ef;
                break;
            case "strain":
                strainOrLine = ef;
                break;
            case "phenotype":
                phenotype = ef;
                break;
        }
    }
    assertNotNull(strainOrLine);
    assertNotNull(phenotype);
    assertNotNull(genotype);
    DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig();
    config.getFactorsToInclude().add(genotype);
    config.getFactorsToInclude().add(phenotype);
    config.setSubsetFactor(strainOrLine);
    analyzer = this.getBean(DiffExAnalyzer.class);
    Collection<DifferentialExpressionAnalysis> result = analyzer.run(ee, config);
    // two subsets
    assertEquals(2, result.size());
}