Uses of Interface
ubic.gemma.model.expression.experiment.BioAssaySetValueObject

Packages that use BioAssaySetValueObject

Package	Description
ubic.gemma.model.analysis.expression.diff
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.rest
ubic.gemma.web.controller.expression.experiment
ubic.gemma.web.controller.visualization

Uses of BioAssaySetValueObject in ubic.gemma.model.analysis.expression.diff

Methods in ubic.gemma.model.analysis.expression.diff that return BioAssaySetValueObject

Modifier and Type	Method	Description
BioAssaySetValueObject	DifferentialExpressionValueObject.getExpressionExperiment()

Methods in ubic.gemma.model.analysis.expression.diff with parameters of type BioAssaySetValueObject

Modifier and Type	Method	Description
void	DifferentialExpressionValueObject.setExpressionExperiment(BioAssaySetValueObject expressionExperiment)

Uses of BioAssaySetValueObject in ubic.gemma.model.expression.experiment

Classes in ubic.gemma.model.expression.experiment that implement BioAssaySetValueObject

Modifier and Type	Class	Description
class	ExpressionExperimentDetailsValueObject
class	ExpressionExperimentSubsetValueObject
class	ExpressionExperimentValueObject

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

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

Modifier and Type	Method	Description
Map<BioAssaySetValueObject,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<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDaoImpl.find(Gene gene, double threshold, int limit)
Map<BioAssaySetValueObject,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<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultService.find(Gene gene)	Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.
Map<BioAssaySetValueObject,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<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultService.find(Gene gene, Collection<Long> experimentsAnalyzed)	Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.
Map<BioAssaySetValueObject,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<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultServiceImpl.find(Collection<Long> experimentsAnalyzed, double threshold, int limit)
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultServiceImpl.find(Gene gene)
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultServiceImpl.find(Gene gene, double threshold, int limit)
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultServiceImpl.find(Gene gene, Collection<Long> experimentsAnalyzed)
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultServiceImpl.find(Gene gene, Collection<Long> experimentsAnalyzed, double threshold, int limit)
Map<BioAssaySetValueObject,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<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDaoImpl.findByExperimentAnalyzed(Collection<Long> experiments, double qvalueThreshold, int limit)
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDao.findByGene(Gene gene)	Find differential expression results for a given gene, grouped by experiment.
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDaoImpl.findByGene(Gene gene)
Map<BioAssaySetValueObject,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<BioAssaySetValueObject,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<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDaoImpl.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentsAnalyzed)
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDaoImpl.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentsAnalyzed, double threshold, int limit)

Uses of BioAssaySetValueObject in ubic.gemma.rest

Classes in ubic.gemma.rest that implement BioAssaySetValueObject

Modifier and Type	Class	Description
static class	DatasetsWebService.ExpressionExperimentSubsetWithFactorValuesObject
static class	DatasetsWebService.ExpressionExperimentSubSetWithGroupsValueObject
static class	DatasetsWebService.ExpressionExperimentWithSearchResultValueObject

Uses of BioAssaySetValueObject in ubic.gemma.web.controller.expression.experiment

Classes in ubic.gemma.web.controller.expression.experiment that implement BioAssaySetValueObject

Modifier and Type	Class	Description
class	ExpressionExperimentEditValueObject

Methods in ubic.gemma.web.controller.expression.experiment that return types with arguments of type BioAssaySetValueObject

Modifier and Type	Method	Description
Map<BioAssaySetValueObject,Map<Long,Collection<DoubleVectorValueObject>>>	DEDVController.getDEDV(Collection<Long> eeIds, Collection<Long> geneIds)	Given a collection of expression experiment Ids and a geneId returns a map of DEDV value objects to a collection of genes.

Uses of BioAssaySetValueObject in ubic.gemma.web.controller.visualization

Methods in ubic.gemma.web.controller.visualization that return BioAssaySetValueObject

Modifier and Type	Method	Description
BioAssaySetValueObject	VisualizationValueObject.getEevo()

Methods in ubic.gemma.web.controller.visualization with parameters of type BioAssaySetValueObject

Modifier and Type	Method	Description
void	VisualizationValueObject.setEevo(BioAssaySetValueObject eevo)
void	VisualizationValueObject.setEEwithPvalue(BioAssaySetValueObject ee, Double minP)