Uses of Class
ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject

Packages that use DifferentialExpressionValueObject

Package	Description
ubic.gemma.core.analysis.expression.diff
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.web.controller.diff

Uses of DifferentialExpressionValueObject in ubic.gemma.core.analysis.expression.diff

Methods in ubic.gemma.core.analysis.expression.diff that return types with arguments of type DifferentialExpressionValueObject

Modifier and Type	Method	Description
Collection<DifferentialExpressionValueObject>	GeneDifferentialExpressionService.getDifferentialExpression(Gene gene, double threshold, int limit)	Get the differential expression results for the given gene across all datasets.
Collection<DifferentialExpressionValueObject>	GeneDifferentialExpressionService.getDifferentialExpression(Gene gene, double threshold, Collection<DiffExpressionSelectedFactorCommand> factorMap)	Get differential expression for a gene, constrained to a specific set of factors.
Collection<DifferentialExpressionValueObject>	GeneDifferentialExpressionService.getDifferentialExpression(Gene gene, Collection<BioAssaySet> ees)	Get the differential expression results for the given gene that is in a specified set of experiments.
Collection<DifferentialExpressionValueObject>	GeneDifferentialExpressionService.getDifferentialExpression(Gene gene, BioAssaySet ees, double threshold, int limit)	Get the differential expression results for the given gene that is in a specified set of experiments.
Collection<DifferentialExpressionValueObject>	GeneDifferentialExpressionServiceImpl.getDifferentialExpression(Gene gene, double threshold, int limit)
Collection<DifferentialExpressionValueObject>	GeneDifferentialExpressionServiceImpl.getDifferentialExpression(Gene gene, double threshold, Collection<DiffExpressionSelectedFactorCommand> factorMap)
Collection<DifferentialExpressionValueObject>	GeneDifferentialExpressionServiceImpl.getDifferentialExpression(Gene gene, Collection<BioAssaySet> ees)
Collection<DifferentialExpressionValueObject>	GeneDifferentialExpressionServiceImpl.getDifferentialExpression(Gene gene, BioAssaySet ee, double threshold, int limit)
Collection<DifferentialExpressionValueObject>	DifferentialExpressionMetaAnalysisValueObject.getProbeResults()

Method parameters in ubic.gemma.core.analysis.expression.diff with type arguments of type DifferentialExpressionValueObject

Modifier and Type	Method	Description
void	DifferentialExpressionMetaAnalysisValueObject.setProbeResults(Collection<DifferentialExpressionValueObject> probeResults)

Uses of DifferentialExpressionValueObject in ubic.gemma.persistence.service.analysis.expression.diff

Methods in ubic.gemma.persistence.service.analysis.expression.diff that return types with arguments of type DifferentialExpressionValueObject

Modifier and Type	Method	Description
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDao.find(Gene gene, double threshold, int limit)	Find differential expression for a gene, exceeding a given significance level (using the corrected pvalue field)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDaoImpl.find(Gene gene, double threshold, int limit)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultService.find(Collection<Long> experimentsAnalyzed, double threshold, int limit)	Given a list of experiments and a threshold value finds all the probes that met the cut off in the given experiments
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultService.find(Gene gene)	Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultService.find(Gene gene, double threshold, int limit)	Find differential expression for a gene, exceeding a given significance level (using the corrected pvalue field)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultService.find(Gene gene, Collection<Long> experimentsAnalyzed)	Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultService.find(Gene gene, Collection<Long> experimentsAnalyzed, double threshold, int limit)	Find differential expression for a gene in given data sets, exceeding a given significance level (using the corrected pvalue field)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultServiceImpl.find(Collection<Long> experimentsAnalyzed, double threshold, int limit)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultServiceImpl.find(Gene gene)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultServiceImpl.find(Gene gene, double threshold, int limit)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultServiceImpl.find(Gene gene, Collection<Long> experimentsAnalyzed)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultServiceImpl.find(Gene gene, Collection<Long> experimentsAnalyzed, double threshold, int limit)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDao.findByExperimentAnalyzed(Collection<Long> experimentsAnalyzed, double threshold, int limit)	Given a list of experiments and a threshold value finds all the probes that met the cut off in the given experiments
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDaoImpl.findByExperimentAnalyzed(Collection<Long> experiments, double qvalueThreshold, int limit)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDao.findByGene(Gene gene)	Find differential expression results for a given gene, grouped by experiment.
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDaoImpl.findByGene(Gene gene)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDao.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentsAnalyzed)	Find differential expression results for a given gene and set of experiments, grouped by experiment.
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDao.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentsAnalyzed, double threshold, int limit)	Find differential expression for a gene in given data sets, exceeding a given significance level (using the corrected pvalue field)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDaoImpl.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentsAnalyzed)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDaoImpl.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentsAnalyzed, double threshold, int limit)
List<DifferentialExpressionValueObject>	DifferentialExpressionResultDao.findInResultSet(ExpressionAnalysisResultSet resultSet, double threshold, int maxResultsToReturn, int minNumberOfResults)
List<DifferentialExpressionValueObject>	DifferentialExpressionResultDaoImpl.findInResultSet(ExpressionAnalysisResultSet resultSet, double threshold, int limit, int minNumberOfResults)
List<DifferentialExpressionValueObject>	DifferentialExpressionResultService.findInResultSet(ExpressionAnalysisResultSet ar, Double threshold, int maxResultsToReturn, int minNumberOfResults)
List<DifferentialExpressionValueObject>	DifferentialExpressionResultServiceImpl.findInResultSet(ExpressionAnalysisResultSet resultSet, Double threshold, int maxResultsToReturn, int minNumberOfResults)
List<DifferentialExpressionValueObject>	DifferentialExpressionResultCache.getTopHits(ExpressionAnalysisResultSet resultSet)
List<DifferentialExpressionValueObject>	DifferentialExpressionResultCacheImpl.getTopHits(ExpressionAnalysisResultSet resultSet)

Method parameters in ubic.gemma.persistence.service.analysis.expression.diff with type arguments of type DifferentialExpressionValueObject

Modifier and Type	Method	Description
void	DifferentialExpressionResultCache.addToTopHitsCache(ExpressionAnalysisResultSet resultSet, List<DifferentialExpressionValueObject> items)
void	DifferentialExpressionResultCacheImpl.addToTopHitsCache(ExpressionAnalysisResultSet resultSet, List<DifferentialExpressionValueObject> items)

Uses of DifferentialExpressionValueObject in ubic.gemma.web.controller.diff

Methods in ubic.gemma.web.controller.diff that return types with arguments of type DifferentialExpressionValueObject

Modifier and Type	Method	Description
Collection<DifferentialExpressionValueObject>	DifferentialExpressionSearchController.getDifferentialExpression(Long geneId, double threshold)	AJAX entry which returns results on a non-meta analysis basis.
Collection<DifferentialExpressionValueObject>	DifferentialExpressionSearchController.getDifferentialExpression(Long geneId, double threshold, Integer limit)	AJAX entry which returns results on a non-meta analysis basis.
Collection<DifferentialExpressionValueObject>	DifferentialExpressionSearchController.getDifferentialExpressionWithoutBatch(Long geneId, double threshold, Integer limit)	AJAX entry which returns results on a non-meta analysis basis.