use of ubic.gemma.model.expression.experiment.ExperimentalFactor in project Gemma by PavlidisLab.
the class VisualizationValueObject method setUpFactorProfiles.
/**
* Initialize the factor profiles.
*/
public void setUpFactorProfiles(LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>> layout) {
if (layout == null) {
VisualizationValueObject.log.warn("Null layout, ignoring");
return;
}
Collection<ExperimentalFactor> efs = new HashSet<>();
for (LinkedHashMap<ExperimentalFactor, Double> maps : layout.values()) {
efs.addAll(maps.keySet());
}
this.factorProfiles = new ArrayList<>();
for (ExperimentalFactor experimentalFactor : efs) {
this.factorProfiles.add(new FactorProfile(experimentalFactor, layout));
}
}
use of ubic.gemma.model.expression.experiment.ExperimentalFactor in project Gemma by PavlidisLab.
the class AncovaTest method testAncovaWithInteraction.
/*
* Two factors with interactions.
*/
@Test
public void testAncovaWithInteraction() {
this.configureMocks();
DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig();
config.getFactorsToInclude().add(this.experimentalFactorA_Area);
config.getFactorsToInclude().add(this.experimentalFactorB);
config.getInteractionsToInclude().add(config.getFactorsToInclude());
Collection<DifferentialExpressionAnalysis> expressionAnalyses = analyzer.run(expressionExperiment, config);
DifferentialExpressionAnalysis expressionAnalysis = expressionAnalyses.iterator().next();
assertNotNull(expressionAnalysis);
Collection<ExpressionAnalysisResultSet> resultSets = expressionAnalysis.getResultSets();
assertEquals(3, resultSets.size());
boolean foundInteractions = false;
boolean foundContrast = false;
for (ExpressionAnalysisResultSet resultSet : resultSets) {
Collection<ExperimentalFactor> factors = resultSet.getExperimentalFactors();
for (DifferentialExpressionAnalysisResult r : resultSet.getResults()) {
CompositeSequence probe = r.getProbe();
Double pvalue = r.getPvalue();
assertNotNull(probe);
Collection<ContrastResult> contrasts = r.getContrasts();
Double stat;
if (contrasts.isEmpty()) {
continue;
}
stat = contrasts.iterator().next().getTstat();
if (factors.size() == 2) {
// interaction
foundInteractions = true;
switch(probe.getName()) {
case "probe_98":
assertEquals(0.7893, pvalue, 0.001);
break;
case "probe_10":
assertEquals(0.04514, pvalue, 0.0001);
break;
case "probe_4":
assertEquals(null, pvalue);
break;
}
} else {
ExperimentalFactor f = factors.iterator().next();
assertNotNull(f);
if (f.equals(super.experimentalFactorA_Area)) {
switch(probe.getName()) {
case "probe_98":
assertEquals(0.8769, pvalue, 0.001);
break;
case "probe_10":
assertEquals(5.158e-10, pvalue, 1e-12);
break;
case "probe_4":
assertEquals(0.0048, pvalue, 0.0001);
assertNotNull(stat);
assertEquals(-125.746, stat, 0.001);
break;
case "probe_0":
assertEquals(1, r.getContrasts().size());
ContrastResult contrast = r.getContrasts().iterator().next();
assertEquals(super.factorValueA1, contrast.getFactorValue());
assertEquals(-202.5587, contrast.getLogFoldChange(), 0.001);
foundContrast = true;
break;
}
} else {
if (probe.getName().equals("probe_98")) {
assertEquals(0.6888, pvalue, 0.001);
} else if (probe.getName().equals("probe_10")) {
assertEquals(0.07970, pvalue, 0.001);
}
}
}
}
}
assertTrue(foundInteractions);
assertTrue(foundContrast);
}
use of ubic.gemma.model.expression.experiment.ExperimentalFactor in project Gemma by PavlidisLab.
the class AncovaTest method testAncovaTriLevel.
/*
* Two fixed-level parameters, one of which has three levels
*/
@Test
public void testAncovaTriLevel() {
this.configureMocks();
/*
* Add a factor with three levels (same one used in onewayanovaanalyzertest)
*/
ExperimentalFactor experimentalFactorC = ExperimentalFactor.Factory.newInstance();
experimentalFactorC.setName("threeLevFactor");
experimentalFactorC.setId(5003L);
experimentalFactorC.setType(FactorType.CATEGORICAL);
expressionExperiment.getExperimentalDesign().getExperimentalFactors().add(experimentalFactorC);
FactorValue fcbase = null;
for (int i = 1; i <= 3; i++) {
FactorValue factorValueC = FactorValue.Factory.newInstance();
factorValueC.setId(2000L + i);
if (i == 3) {
factorValueC.setValue("control_group");
fcbase = factorValueC;
} else {
factorValueC.setValue(i + "_group");
}
factorValueC.setExperimentalFactor(experimentalFactorC);
experimentalFactorC.getFactorValues().add(factorValueC);
}
List<FactorValue> facV = new ArrayList<>(experimentalFactorC.getFactorValues());
for (int i = 0; i < 8; i++) {
super.biomaterials.get(i).getFactorValues().add(facV.get(i % 3));
}
List<ExperimentalFactor> factors = new ArrayList<>();
factors.add(experimentalFactorA_Area);
factors.add(experimentalFactorC);
DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig();
config.setFactorsToInclude(factors);
Collection<DifferentialExpressionAnalysis> expressionAnalyses = analyzer.run(expressionExperiment, config);
DifferentialExpressionAnalysis expressionAnalysis = expressionAnalyses.iterator().next();
assertNotNull(expressionAnalysis);
Collection<ExpressionAnalysisResultSet> resultSets = expressionAnalysis.getResultSets();
assertEquals(2, resultSets.size());
boolean found14 = false;
boolean found198 = false;
boolean found3 = false;
boolean found4 = false;
for (ExpressionAnalysisResultSet resultSet : resultSets) {
assertEquals(1, resultSet.getExperimentalFactors().size());
log.info(resultSet.getBaselineGroup());
assertTrue(resultSet.getBaselineGroup().equals(factorValueA2) || resultSet.getBaselineGroup().equals(fcbase));
ExperimentalFactor f = resultSet.getExperimentalFactors().iterator().next();
for (DifferentialExpressionAnalysisResult r : resultSet.getResults()) {
CompositeSequence probe = r.getProbe();
Double pvalue = r.getPvalue();
if (f.equals(super.experimentalFactorA_Area)) {
if (probe.getName().equals("probe_98")) {
assertEquals(0.8060, pvalue, 0.001);
found198 = true;
}
} else if (probe.getName().equals("probe_10")) {
assertEquals(0.9088, pvalue, 0.001);
found3 = true;
}
Collection<ContrastResult> contrasts = r.getContrasts();
Double stat;
if (contrasts.isEmpty()) {
continue;
}
stat = contrasts.iterator().next().getTstat();
assertNotNull(probe);
if (stat == null)
continue;
if (f.equals(super.experimentalFactorA_Area)) {
if (probe.getName().equals("probe_10")) {
assertEquals(9.215e-09, pvalue, 1e-11);
assertEquals(-152.812, stat, 0.001);
} else if (probe.getName().equals("probe_4")) {
assertEquals(0.006278, pvalue, 0.0001);
assertEquals(-95.118, stat, 0.001);
found14 = true;
}
} else {
if (contrasts.size() == 2) {
found4 = true;
}
if (probe.getName().equals("probe_98")) {
assertEquals(0.2171, pvalue, 0.001);
}
}
}
}
assertTrue("Didn't find results", found14 && found198 && found3);
assertTrue("Didn't find the right number of contrasts", found4);
}
use of ubic.gemma.model.expression.experiment.ExperimentalFactor in project Gemma by PavlidisLab.
the class AncovaTest method testAncovaCovariate.
/*
* With a continuous covariate + two categorical
*/
@Test
public void testAncovaCovariate() {
this.configureMocks();
/*
* Add a continuous factor
*/
ExperimentalFactor experimentalFactorC = ExperimentalFactor.Factory.newInstance();
experimentalFactorC.setName("confabulatiliationity");
experimentalFactorC.setId(5399424551L);
experimentalFactorC.setType(FactorType.CONTINUOUS);
this.setupFactorValues(experimentalFactorC);
expressionExperiment.getExperimentalDesign().getExperimentalFactors().add(experimentalFactorC);
DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig();
config.setFactorsToInclude(expressionExperiment.getExperimentalDesign().getExperimentalFactors());
Collection<DifferentialExpressionAnalysis> expressionAnalyses = analyzer.run(expressionExperiment, config);
DifferentialExpressionAnalysis expressionAnalysis = expressionAnalyses.iterator().next();
assertNotNull(expressionAnalysis);
Collection<ExpressionAnalysisResultSet> resultSets = expressionAnalysis.getResultSets();
assertEquals(3, resultSets.size());
for (ExpressionAnalysisResultSet resultSet : resultSets) {
Collection<ExperimentalFactor> factors = resultSet.getExperimentalFactors();
assertEquals(1, factors.size());
for (DifferentialExpressionAnalysisResult r : resultSet.getResults()) {
CompositeSequence probe = r.getProbe();
Double pvalue = r.getPvalue();
assertNotNull(probe);
// log.debug( "probe: " + probe + "; Factor="
// + resultSet.getExperimentalFactors().iterator().next().getName() + "; p-value: " + pvalue
// + "; T=" + stat );
ExperimentalFactor f = factors.iterator().next();
if (f.equals(super.experimentalFactorA_Area)) {
switch(probe.getName()) {
case "probe_98":
assertEquals(0.8673, pvalue, 0.001);
break;
case "probe_10":
assertEquals(4.062e-09, pvalue, 1e-10);
break;
case "probe_4":
// too few samples
assertEquals(null, pvalue);
// assertEquals( null, stat );
break;
}
} else if (f.equals(super.experimentalFactorB)) {
if (probe.getName().equals("probe_98")) {
assertEquals(0.6665, pvalue, 0.001);
} else if (probe.getName().equals("probe_10")) {
assertEquals(0.2356, pvalue, 0.001);
}
} else {
// our new one.
if (probe.getName().equals("probe_98")) {
assertEquals(0.4977, pvalue, 0.001);
} else if (probe.getName().equals("probe_10")) {
assertEquals(0.57347, pvalue, 0.001);
}
}
}
}
}
use of ubic.gemma.model.expression.experiment.ExperimentalFactor in project Gemma by PavlidisLab.
the class AncovaTest method testAncovaTwoway.
/*
* Two fixed-level parameters
*/
@Test
public void testAncovaTwoway() {
this.configureMocks();
DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig();
config.setFactorsToInclude(super.experimentalFactors);
Collection<DifferentialExpressionAnalysis> expressionAnalyses = analyzer.run(expressionExperiment, config);
DifferentialExpressionAnalysis expressionAnalysis = expressionAnalyses.iterator().next();
assertNotNull(expressionAnalysis);
Collection<ExpressionAnalysisResultSet> resultSets = expressionAnalysis.getResultSets();
assertEquals(2, resultSets.size());
for (ExpressionAnalysisResultSet resultSet : resultSets) {
Collection<ExperimentalFactor> factors = resultSet.getExperimentalFactors();
assertEquals(1, factors.size());
for (DifferentialExpressionAnalysisResult probeAnalysisResult : resultSet.getResults()) {
CompositeSequence probe = probeAnalysisResult.getProbe();
Double pvalue = probeAnalysisResult.getPvalue();
Collection<ContrastResult> contrasts = probeAnalysisResult.getContrasts();
Double stat;
if (contrasts.isEmpty()) {
continue;
}
stat = contrasts.iterator().next().getTstat();
assertNotNull(probe);
// log.debug( "probe: " + probe + "; p-value: " + pvalue + "; T=" + stat );
ExperimentalFactor f = factors.iterator().next();
if (f.equals(super.experimentalFactorA_Area)) {
switch(probe.getName()) {
case "probe_98":
assertEquals(0.8572, pvalue, 0.001);
break;
case "probe_10":
assertEquals(4.69e-11, pvalue, 1e-12);
break;
case "probe_4":
assertEquals(0.0048, pvalue, 0.0001);
assertNotNull(stat);
assertEquals(-125.746, stat, 0.001);
// factor1a
assertEquals(0.00506, contrasts.iterator().next().getPvalue(), 0.0001);
break;
}
} else {
if (probe.getName().equals("probe_98")) {
assertEquals(0.6417, pvalue, 0.001);
} else if (probe.getName().equals("probe_10")) {
assertEquals(0.196, pvalue, 0.001);
}
}
}
}
}
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