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

Example 26 with BioAssaySet

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

the class ExpressionExperimentSetServiceImpl method updateDatabaseEntityMembers.

/**
 * update the members of the experiment set with the given ids
 *
 * @param groupId set to update
 * @param eeIds   new set member ids
 */
@Override
@Transactional
public void updateDatabaseEntityMembers(Long groupId, Collection<Long> eeIds) {
    if (eeIds.isEmpty()) {
        throw new IllegalArgumentException("No expression experiment ids provided. Cannot save an empty set.");
    }
    ExpressionExperimentSet eeSet = this.load(groupId);
    if (eeSet == null) {
        throw new IllegalArgumentException("No experiment set with id=" + groupId + " could be loaded. " + "Either it does not exist or you do not have permission to view it.");
    }
    // check that new member ids are valid
    Collection<ExpressionExperiment> newExperiments = expressionExperimentService.load(eeIds);
    if (newExperiments.isEmpty()) {
        throw new IllegalArgumentException("None of the experiment ids were valid (out of " + eeIds.size() + " provided)");
    }
    if (newExperiments.size() < eeIds.size()) {
        throw new IllegalArgumentException("Some of the experiment ids were invalid: only found " + newExperiments.size() + " out of " + eeIds.size() + " provided)");
    }
    assert newExperiments.size() == eeIds.size();
    Collection<BioAssaySet> basColl = new HashSet<>();
    for (ExpressionExperiment experiment : newExperiments) {
        Taxon eeTaxon = this.getTaxonForSet(experiment);
        // make sure experiments being added are from the right taxon
        if (eeTaxon == null || !eeTaxon.equals(eeSet.getTaxon())) {
            throw new IllegalArgumentException(experiment + " is of the wrong taxon to add to eeset. EESet taxon is " + eeSet.getTaxon());
        }
        basColl.add(experiment);
    }
    eeSet.getExperiments().clear();
    eeSet.getExperiments().addAll(basColl);
    this.update(eeSet);
}

Example 27 with BioAssaySet

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

the class ExpressionExperimentSetServiceImpl method update.

/**
 * @see ExpressionExperimentSetService#update(ExpressionExperimentSet)
 */
@Override
@Transactional
public void update(final ExpressionExperimentSet expressionExperimentSet) {
    if (expressionExperimentSet == null) {
        throw new IllegalArgumentException("Cannot update null set");
    }
    if (expressionExperimentSet.getId() == null || expressionExperimentSet.getId() < 0) {
        throw new IllegalArgumentException("Can only update an existing eeset (passed id=" + expressionExperimentSet.getId() + ")");
    }
    if (StringUtils.isBlank(expressionExperimentSet.getName())) {
        throw new IllegalArgumentException("You must provide a name");
    }
    // make sure potentially new experiment members are of the right taxon
    Taxon groupTaxon = expressionExperimentSet.getTaxon();
    Taxon eeTaxon;
    for (BioAssaySet ee : expressionExperimentSet.getExperiments()) {
        eeTaxon = this.getTaxonForSet(ee);
        assert eeTaxon != null;
        if (!eeTaxon.equals(groupTaxon)) {
            throw new IllegalArgumentException("Failed to add experiments of wrong taxa (" + ee + ") to eeset. " + "EESet taxon is " + groupTaxon + ", experiment was " + eeTaxon);
        }
    }
    if (StringUtils.isBlank(expressionExperimentSet.getName())) {
        throw new IllegalArgumentException("Attempt to update an ExpressionExperimentSet so it has no name");
    }
    this.expressionExperimentSetDao.update(expressionExperimentSet);
}

Example 28 with BioAssaySet

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

the class ProcessedExpressionDataVectorServiceImpl method getDiffExVectors.

@Override
public List<DoubleVectorValueObject> getDiffExVectors(Long resultSetId, Double threshold, int maxNumberOfResults) {
    ExpressionAnalysisResultSet ar = differentialExpressionResultService.loadAnalysisResultSet(resultSetId);
    if (ar == null) {
        Log.warn(this.getClass(), "No diff ex result set with ID=" + resultSetId);
        return null;
    }
    differentialExpressionResultService.thawLite(ar);
    BioAssaySet analyzedSet = ar.getAnalysis().getExperimentAnalyzed();
    List<DifferentialExpressionValueObject> ee2probeResults = differentialExpressionResultService.findInResultSet(ar, threshold, maxNumberOfResults, ProcessedExpressionDataVectorServiceImpl.DIFFEX_MIN_NUMBER_OF_RESULTS);
    Collection<Long> probes = new HashSet<>();
    // Map<CompositeSequenceId, pValue>
    // using id instead of entity for map key because want to use a value object for retrieval later
    Map<Long, Double> pvalues = new HashMap<>();
    for (DifferentialExpressionValueObject par : ee2probeResults) {
        probes.add(par.getProbeId());
        pvalues.put(par.getProbeId(), par.getP());
    }
    Collection<DoubleVectorValueObject> processedDataArraysByProbe = this.getProcessedDataArraysByProbeIds(analyzedSet, probes);
    List<DoubleVectorValueObject> dedvs = new ArrayList<>(processedDataArraysByProbe);
    /*
         * Resort
         */
    for (DoubleVectorValueObject v : dedvs) {
        v.setPvalue(pvalues.get(v.getDesignElement().getId()));
    }
    Collections.sort(dedvs, new Comparator<DoubleVectorValueObject>() {

        @Override
        public int compare(DoubleVectorValueObject o1, DoubleVectorValueObject o2) {
            if (o1.getPvalue() == null)
                return -1;
            if (o2.getPvalue() == null)
                return 1;
            return o1.getPvalue().compareTo(o2.getPvalue());
        }
    });
    return dedvs;
}

Example 29 with BioAssaySet

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

the class ProcessedExpressionDataVectorDaoImpl method getExperiments.

/**
 * Determine the experiments that bioAssaySets refer to.
 *
 * @param bioAssaySets - either ExpressionExperiment or ExpressionExperimentSubSet (which has an associated
 *                     ExpressionExperiment, which is what we're after)
 * @return Note that this collection can be smaller than the input, if two bioAssaySets come from (or are) the same
 * Experiment
 */
private Collection<ExpressionExperiment> getExperiments(Collection<? extends BioAssaySet> bioAssaySets) {
    Collection<ExpressionExperiment> result = new HashSet<>();
    for (BioAssaySet bas : bioAssaySets) {
        ExpressionExperiment e = this.getExperiment(bas);
        result.add(e);
    }
    return result;
}

Example 30 with BioAssaySet

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

the class LinkAnalysisServiceTest method testLoadAnalyzeSaveAndCoexpSearch.

@Test
public void testLoadAnalyzeSaveAndCoexpSearch() {
    ee = this.getTestPersistentCompleteExpressionExperimentWithSequences();
    processedExpressionDataVectorService.computeProcessedExpressionData(ee);
    tableMaintenanceUtil.disableEmail();
    tableMaintenanceUtil.updateGene2CsEntries();
    linkAnalysisConfig.setCdfCut(0.1);
    linkAnalysisConfig.setSingularThreshold(SingularThreshold.cdfcut);
    linkAnalysisConfig.setProbeDegreeThreshold(25);
    linkAnalysisConfig.setCheckCorrelationDistribution(false);
    linkAnalysisConfig.setCheckForBatchEffect(false);
    filterConfig.setIgnoreMinimumSampleThreshold(true);
    // first time.
    // noinspection UnusedAssignment // we still want to do this for the testing sake
    LinkAnalysis la = linkAnalysisService.process(ee, filterConfig, linkAnalysisConfig);
    // test remove is clean; to check this properly requires checking the db.
    linkAnalysisPersisterService.deleteAnalyses(ee);
    this.checkUnsupportedLinksHaveNoSupport();
    assertEquals(0, geneCoexpressionService.getCoexpression(ee, true).size());
    la = linkAnalysisService.process(ee, filterConfig, linkAnalysisConfig);
    CoexpressionAnalysis analysisObj = la.getAnalysisObj();
    assertEquals(151, analysisObj.getNumberOfElementsAnalyzed().intValue());
    assertTrue(analysisObj.getNumberOfLinks() > 0);
    assertNotNull(analysisObj.getCoexpCorrelationDistribution());
    Collection<BioAssaySet> ees = new HashSet<>();
    ees.add(ee);
    this.updateNodeDegree();
    int totalLinksFirstPass = this.checkResults(ees, 1);
    // should be ~1140.
    assertTrue(totalLinksFirstPass > 1000);
    // test redo
    linkAnalysisService.process(ee, filterConfig, linkAnalysisConfig);
    this.updateNodeDegree();
    int totalLinksRedo = this.checkResults(ees, 1);
    assertEquals(totalLinksFirstPass, totalLinksRedo);
    // now add another experiment that has overlapping links (same data...
    Map<CompositeSequence, byte[]> dataMap = new HashMap<>();
    ee = eeService.thaw(ee);
    for (RawExpressionDataVector v : ee.getRawExpressionDataVectors()) {
        dataMap.put(v.getDesignElement(), v.getData());
    }
    ExpressionExperiment ee2 = this.getTestPersistentCompleteExpressionExperimentWithSequences(ee);
    // eeService.thawRawAndProcessed( ee2 );
    for (RawExpressionDataVector v : ee2.getRawExpressionDataVectors()) {
        assert dataMap.get(v.getDesignElement()) != null;
        v.setData(dataMap.get(v.getDesignElement()));
    }
    eeService.update(ee2);
    processedExpressionDataVectorService.computeProcessedExpressionData(ee2);
    linkAnalysisService.process(ee2, filterConfig, linkAnalysisConfig);
    this.updateNodeDegree();
    // expect to get at least one links with support >1
    ees.add(ee2);
    this.checkResults(ees, 2);
}