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

Example 11 with ExperimentalFactor

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

the class TwoWayAnovaWithInteractionsAnalyzerTest method checkResults.

/**
 * @param resultSet the result set to check
 */
private void checkResults(ExpressionAnalysisResultSet resultSet) {
    Collection<ExperimentalFactor> factors = resultSet.getExperimentalFactors();
    for (DifferentialExpressionAnalysisResult r : resultSet.getResults()) {
        CompositeSequence probe = r.getProbe();
        Double pvalue = r.getPvalue();
        pvalue = pvalue == null ? Double.NaN : pvalue;
        Double qvalue = r.getCorrectedPvalue();
        assertNotNull(probe);
        if (factors.size() == 1) {
            ExperimentalFactor f = factors.iterator().next();
            if (f.equals(super.experimentalFactorA_Area)) {
                assertEquals(factorValueA2, resultSet.getBaselineGroup());
                switch(probe.getName()) {
                    case "probe_98":
                        assertEquals(0.8769, pvalue, 0.001);
                        assertNotNull(qvalue);
                        break;
                    case "probe_10":
                        assertEquals(5.158e-10, pvalue, 1e-12);
                        break;
                    case "probe_4":
                        assertEquals(0.0048, pvalue, 0.0001);
                        break;
                }
            } else {
                assertEquals(factorValueB2, resultSet.getBaselineGroup());
                if (probe.getName().equals("probe_98")) {
                    assertEquals(0.6888, pvalue, 0.001);
                } else if (probe.getName().equals("probe_10")) {
                    assertEquals(0.07970, pvalue, 0.00001);
                }
            }
        } else {
            assertEquals(null, resultSet.getBaselineGroup());
            switch(probe.getName()) {
                case "probe_98":
                    assertEquals(0.7893, pvalue, 0.001);
                    break;
                case "probe_10":
                    assertEquals(0.04514, pvalue, 0.00001);
                    break;
                case "probe_4":
                    assertEquals(Double.NaN, pvalue, 0.00001);
                    break;
            }
        }
    }
}

Example 12 with ExperimentalFactor

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

the class TwoWayAnovaWithInteractionsAnalyzerTest method testTwoWayAnova.

@Test
public void testTwoWayAnova() {
    log.debug("Testing TwoWayAnova method in " + DiffExAnalyzer.class.getName());
    if (!connected) {
        log.warn("Could not establish R connection.  Skipping test ...");
        return;
    }
    this.configureMocks();
    Collection<ExperimentalFactor> factors = new HashSet<>();
    factors.add(experimentalFactorA_Area);
    factors.add(experimentalFactorB);
    DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig();
    config.setFactorsToInclude(factors);
    config.addInteractionToInclude(factors);
    Collection<DifferentialExpressionAnalysis> expressionAnalyses = analyzer.run(expressionExperiment, config);
    DifferentialExpressionAnalysis expressionAnalysis = expressionAnalyses.iterator().next();
    Collection<ExpressionAnalysisResultSet> resultSets = expressionAnalysis.getResultSets();
    assertEquals(BaseAnalyzerConfigurationTest.NUM_TWA_RESULT_SETS, resultSets.size());
    for (ExpressionAnalysisResultSet resultSet : resultSets) {
        this.checkResults(resultSet);
    }
}

Example 13 with ExperimentalFactor

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

the class TwoWayAnovaWithoutInteractionsAnalyzerTest method testTwoWayAnova.

/**
 * Tests the TwoWayAnova method.
 */
@Test
public void testTwoWayAnova() {
    log.debug("Testing getPValues method in " + DiffExAnalyzer.class.getName());
    if (!connected) {
        log.warn("Could not establish R connection.  Skipping test ...");
        return;
    }
    this.configureMocks();
    List<ExperimentalFactor> factors = Arrays.asList(experimentalFactorA_Area, experimentalFactorB);
    DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig();
    config.setFactorsToInclude(factors);
    Collection<DifferentialExpressionAnalysis> expressionAnalyses = analyzer.run(expressionExperiment, config);
    DifferentialExpressionAnalysis expressionAnalysis = expressionAnalyses.iterator().next();
    Collection<ExpressionAnalysisResultSet> resultSets = expressionAnalysis.getResultSets();
    assertEquals(2, resultSets.size());
    for (ExpressionAnalysisResultSet resultSet : resultSets) {
        this.checkResults(resultSet);
    }
}

Example 14 with ExperimentalFactor

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

the class TwoWayAnovaWithoutInteractionsAnalyzerTest method checkResults.

/**
 * @param resultSet the result set to check
 */
private void checkResults(ExpressionAnalysisResultSet resultSet) {
    Collection<ExperimentalFactor> factors = resultSet.getExperimentalFactors();
    assertEquals("Should not have an interaction term", 1, factors.size());
    ExperimentalFactor f = factors.iterator().next();
    boolean found = false;
    for (DifferentialExpressionAnalysisResult r : resultSet.getResults()) {
        CompositeSequence probe = r.getProbe();
        Double pvalue = r.getPvalue();
        if (f.equals(super.experimentalFactorB) && probe.getName().equals("probe_1")) {
            assertEquals(0.501040, pvalue, 0.001);
            found = true;
        }
        Collection<ContrastResult> contrasts = r.getContrasts();
        Double stat;
        if (contrasts.isEmpty()) {
            continue;
        }
        stat = contrasts.iterator().next().getTstat();
        assertNotNull(probe);
        if (f.equals(super.experimentalFactorA_Area)) {
            assertEquals(factorValueA2, resultSet.getBaselineGroup());
            switch(probe.getName()) {
                case // id=1001
                "probe_1":
                    assertEquals(0.001814, pvalue, 0.00001);
                    assertNotNull(stat);
                    assertEquals(-287.061, stat, 0.001);
                    found = true;
                    break;
                case // id 1097
                "probe_97":
                    assertEquals(0.3546, pvalue, 0.001);
                    break;
                case "probe_0":
                    assertEquals(1.36e-12, pvalue, 1e-10);
                    assertNotNull(stat);
                    assertEquals(-425.3, stat, 0.1);
                    break;
            }
        } else {
            assertEquals(factorValueB2, resultSet.getBaselineGroup());
            if (probe.getName().equals("probe_97")) {
                assertEquals(0.4449, pvalue, 0.001);
            }
        }
    }
    assertTrue("Did not find expected results for probe_1", found);
}

Example 15 with ExperimentalFactor

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

the class DatabaseViewGeneratorImpl method generateDifferentialExpressionView.

private void generateDifferentialExpressionView(Integer limit, Collection<ExpressionExperiment> experiments) throws IOException {
    DatabaseViewGeneratorImpl.log.info("Generating dataset diffex view");
    /*
         * Get handle to output file
         */
    File file = this.getViewFile(DatabaseViewGeneratorImpl.DATASET_DIFFEX_VIEW_BASENAME);
    DatabaseViewGeneratorImpl.log.info("Writing to " + file);
    try (Writer writer = new OutputStreamWriter(new GZIPOutputStream(new FileOutputStream(file)))) {
        /*
             * For each gene that is differentially expressed, print out a line per contrast
             */
        writer.write("GemmaDsId\tEEShortName\tGeneNCBIId\tGemmaGeneId\tFactor\tFactorURI\tBaseline\tContrasting\tDirection\n");
        int i = 0;
        for (ExpressionExperiment ee : experiments) {
            ee = expressionExperimentService.thawLite(ee);
            Collection<DifferentialExpressionAnalysis> results = differentialExpressionAnalysisService.getAnalyses(ee);
            if (results == null || results.isEmpty()) {
                DatabaseViewGeneratorImpl.log.warn("No differential expression results found for " + ee);
                continue;
            }
            // noinspection StatementWithEmptyBody // FIXME. Should probably skip for this purpose.
            if (results.size() > 1) {
            }
            DatabaseViewGeneratorImpl.log.info("Processing: " + ee.getShortName());
            for (DifferentialExpressionAnalysis analysis : results) {
                analysis = this.differentialExpressionAnalysisService.thawFully(analysis);
                for (ExpressionAnalysisResultSet ears : analysis.getResultSets()) {
                    // ears = differentialExpressionResultService.thawRawAndProcessed( ears );
                    FactorValue baselineGroup = ears.getBaselineGroup();
                    if (baselineGroup == null) {
                        // log.warn( "No baseline defined for " + ee ); // interaction
                        continue;
                    }
                    if (ExperimentalDesignUtils.isBatch(baselineGroup.getExperimentalFactor())) {
                        continue;
                    }
                    String baselineDescription = ExperimentalDesignUtils.prettyString(baselineGroup);
                    // Get the factor category name
                    StringBuilder factorName = new StringBuilder();
                    StringBuilder factorURI = new StringBuilder();
                    for (ExperimentalFactor ef : ears.getExperimentalFactors()) {
                        factorName.append(ef.getName()).append(",");
                        if (ef.getCategory() instanceof VocabCharacteristic) {
                            factorURI.append(ef.getCategory().getCategoryUri()).append(",");
                        }
                    }
                    factorName = new StringBuilder(StringUtils.removeEnd(factorName.toString(), ","));
                    factorURI = new StringBuilder(StringUtils.removeEnd(factorURI.toString(), ","));
                    if (ears.getResults() == null || ears.getResults().isEmpty()) {
                        DatabaseViewGeneratorImpl.log.warn("No  differential expression analysis results found for " + ee);
                        continue;
                    }
                    // Generate probe details
                    for (DifferentialExpressionAnalysisResult dear : ears.getResults()) {
                        if (dear == null) {
                            DatabaseViewGeneratorImpl.log.warn("Missing results for " + ee + " skipping to next. ");
                            continue;
                        }
                        if (dear.getCorrectedPvalue() == null || dear.getCorrectedPvalue() > DatabaseViewGeneratorImpl.THRESH_HOLD)
                            continue;
                        String formatted = this.formatDiffExResult(ee, dear, factorName.toString(), factorURI.toString(), baselineDescription);
                        if (StringUtils.isNotBlank(formatted))
                            writer.write(formatted);
                    }
                // dear loop
                }
            // ears loop
            }
            if (limit != null && (limit > 0 && ++i > limit))
                break;
        }
    // EE loop
    }
}