Uses of Class
ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject

Packages that use ExpressionExperimentValueObject

Package	Description
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.tasks.visualization
ubic.gemma.model.analysis.expression.diff
ubic.gemma.model.common.description
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.rest
ubic.gemma.rest.util.args
ubic.gemma.web.controller.expression.experiment
ubic.gemma.web.controller.visualization

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

Methods in ubic.gemma.core.analysis.expression.diff that return ExpressionExperimentValueObject

Modifier and Type	Method	Description
ExpressionExperimentValueObject	GeneDifferentialExpressionService.configExpressionExperimentValueObject(ExpressionExperimentValueObject ee)
ExpressionExperimentValueObject	GeneDifferentialExpressionServiceImpl.configExpressionExperimentValueObject(ExpressionExperimentValueObject ee)

Methods in ubic.gemma.core.analysis.expression.diff with parameters of type ExpressionExperimentValueObject

Modifier and Type	Method	Description
ExpressionExperimentValueObject	GeneDifferentialExpressionService.configExpressionExperimentValueObject(ExpressionExperimentValueObject ee)
ExpressionExperimentValueObject	GeneDifferentialExpressionServiceImpl.configExpressionExperimentValueObject(ExpressionExperimentValueObject ee)

Uses of ExpressionExperimentValueObject in ubic.gemma.core.tasks.visualization

Constructors in ubic.gemma.core.tasks.visualization with parameters of type ExpressionExperimentValueObject

Constructor	Description
Condition(ExpressionExperimentValueObject experiment, DifferentialExpressionAnalysisValueObject analysis, DiffExResultSetSummaryValueObject resultSet, FactorValueValueObject factorValue)

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

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

Modifier and Type	Method	Description
ExpressionExperimentValueObject	DifferentialExpressionValueObject.getExpressionExperiment()

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

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

Uses of ExpressionExperimentValueObject in ubic.gemma.model.common.description

Methods in ubic.gemma.model.common.description that return types with arguments of type ExpressionExperimentValueObject

Modifier and Type	Method	Description
Collection<ExpressionExperimentValueObject>	BibliographicReferenceValueObject.getExperiments()

Method parameters in ubic.gemma.model.common.description with type arguments of type ExpressionExperimentValueObject

Modifier and Type	Method	Description
void	BibliographicReferenceValueObject.setExperiments(Collection<ExpressionExperimentValueObject> experiments)

Constructor parameters in ubic.gemma.model.common.description with type arguments of type ExpressionExperimentValueObject

Constructor	Description
BibliographicReferenceValueObject(Long id, String abstractText, String authorList, String issue, String pages, String pubAccession, String publication, Date publicationDate, String publisher, String title, String volume, Collection<ExpressionExperimentValueObject> experiments)

Uses of ExpressionExperimentValueObject in ubic.gemma.model.expression.bioAssayData

Methods in ubic.gemma.model.expression.bioAssayData that return ExpressionExperimentValueObject

Modifier and Type	Method	Description
ExpressionExperimentValueObject	DataVectorValueObject.getExpressionExperiment()

Methods in ubic.gemma.model.expression.bioAssayData with parameters of type ExpressionExperimentValueObject

Modifier and Type	Method	Description
void	DataVectorValueObject.setExpressionExperiment(ExpressionExperimentValueObject expressionExperiment)

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

Subclasses of ExpressionExperimentValueObject in ubic.gemma.model.expression.experiment

Modifier and Type	Class	Description
class	ExpressionExperimentDetailsValueObject
class	ExpressionExperimentSubsetValueObject

Methods in ubic.gemma.model.expression.experiment that return ExpressionExperimentValueObject

Modifier and Type	Method	Description
abstract ExpressionExperimentValueObject	BioAssaySet.createValueObject()	Special use case.
ExpressionExperimentValueObject	ExpressionExperiment.createValueObject()
ExpressionExperimentValueObject	ExpressionExperimentSubSet.createValueObject()

Methods in ubic.gemma.model.expression.experiment that return types with arguments of type ExpressionExperimentValueObject

Modifier and Type	Method	Description
Collection<ExpressionExperimentValueObject>	ExpressionExperimentDetailsValueObject.getOtherParts()

Method parameters in ubic.gemma.model.expression.experiment with type arguments of type ExpressionExperimentValueObject

Modifier and Type	Method	Description
void	ExpressionExperimentDetailsValueObject.setOtherParts(Collection<ExpressionExperimentValueObject> otherParts)

Constructors in ubic.gemma.model.expression.experiment with parameters of type ExpressionExperimentValueObject

Constructor	Description
ExpressionExperimentDetailsValueObject(ExpressionExperimentValueObject vo)
ExpressionExperimentValueObject(ExpressionExperimentValueObject vo)

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

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

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)

Uses of ExpressionExperimentValueObject in ubic.gemma.persistence.service.expression.experiment

Methods in ubic.gemma.persistence.service.expression.experiment that return ExpressionExperimentValueObject

Modifier and Type	Method	Description
protected ExpressionExperimentValueObject	ExpressionExperimentDaoImpl.doLoadValueObject(ExpressionExperiment entity)

Methods in ubic.gemma.persistence.service.expression.experiment that return types with arguments of type ExpressionExperimentValueObject

Modifier and Type	Method	Description
protected TypedResultTransformer<ExpressionExperimentValueObject>	ExpressionExperimentDaoImpl.getValueObjectTransformer()
Slice<ExpressionExperimentValueObject>	ExpressionExperimentDao.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentDaoImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentService.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentServiceImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
List<ExpressionExperimentValueObject>	ExpressionExperimentDaoImpl.loadValueObjects(Filters filters, Sort sort)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentDaoImpl.loadValueObjects(Filters filters, Sort sort, int offset, int limit)
List<ExpressionExperimentValueObject>	ExpressionExperimentService.loadValueObjectsByIds(List<Long> ids, boolean maintainOrder)	Variant of BaseVoEnabledService.loadValueObjectsByIds(Collection) that preserve its input order.
List<ExpressionExperimentValueObject>	ExpressionExperimentServiceImpl.loadValueObjectsByIds(List<Long> ids, boolean maintainOrder)
List<ExpressionExperimentValueObject>	ExpressionExperimentService.loadValueObjectsByIdsWithRelationsAndCache(List<Long> ids)	Load VOs for the given dataset IDs and initialize their relations like SecurableFilteringVoEnabledService.load(Filters, Sort).
List<ExpressionExperimentValueObject>	ExpressionExperimentServiceImpl.loadValueObjectsByIdsWithRelationsAndCache(List<Long> ids)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentService.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentServiceImpl.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit)
Collection<ExpressionExperimentValueObject>	ExpressionExperimentSearchService.searchExpressionExperiments(String query)
Collection<ExpressionExperimentValueObject>	ExpressionExperimentSearchService.searchExpressionExperiments(List<String> value)
Collection<ExpressionExperimentValueObject>	ExpressionExperimentSearchServiceImpl.searchExpressionExperiments(String query)
Collection<ExpressionExperimentValueObject>	ExpressionExperimentSearchServiceImpl.searchExpressionExperiments(List<String> query)

Method parameters in ubic.gemma.persistence.service.expression.experiment with type arguments of type ExpressionExperimentValueObject

Modifier and Type	Method	Description
protected void	ExpressionExperimentDaoImpl.postProcessValueObjects(List<ExpressionExperimentValueObject> results)

Uses of ExpressionExperimentValueObject in ubic.gemma.rest

Subclasses of ExpressionExperimentValueObject in ubic.gemma.rest

Modifier and Type	Class	Description
static class	DatasetsWebService.ExpressionExperimentWithSearchResultValueObject

Methods in ubic.gemma.rest that return types with arguments of type ExpressionExperimentValueObject

Modifier and Type	Method	Description
DatasetsWebService.FilteredAndInferredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	DatasetsWebService.getBlacklistedDatasets(FilterArg<ExpressionExperiment> filterArg, SortArg<ExpressionExperiment> sortArg, OffsetArg offset, LimitArg limit)	Browse blacklisted datasets.
DatasetsWebService.FilteredAndInferredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	DatasetsWebService.getDatasetsByIds(DatasetArrayArg datasetsArg, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort)	Retrieves all datasets matching the given identifiers.
PaginatedResponseDataObject<ExpressionExperimentValueObject>	PlatformsWebService.getPlatformDatasets(PlatformArg<?> platformArg, OffsetArg offset, LimitArg limit)	Retrieves experiments in the given platform.
FilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	TaxaWebService.getTaxonDatasets(TaxonArg<?> taxonArg, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort)	Retrieves datasets for the given taxon.
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	AnnotationsWebService.searchDatasets(StringArrayArg query, FilterArg<ExpressionExperiment> filterArg, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sortArg)	Does a search for datasets containing characteristics matching the given string.
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	AnnotationsWebService.searchDatasetsByQueryInPath(StringArrayArg query, FilterArg<ExpressionExperiment> filterArg, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sortArg)
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	AnnotationsWebService.searchTaxonDatasets(TaxonArg<?> taxonArg, StringArrayArg query, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort)	Same as AnnotationsWebService.searchDatasets(StringArrayArg, FilterArg, OffsetArg, LimitArg, SortArg) but also filters by taxon.
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	AnnotationsWebService.searchTaxonDatasetsByQueryInPath(TaxonArg<?> taxonArg, StringArrayArg query, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort)

Constructors in ubic.gemma.rest with parameters of type ExpressionExperimentValueObject

Constructor	Description
ExpressionExperimentWithSearchResultValueObject(ExpressionExperimentValueObject vo, SearchResult<ExpressionExperiment> result)

Uses of ExpressionExperimentValueObject in ubic.gemma.rest.util.args

Methods in ubic.gemma.rest.util.args that return types with arguments of type ExpressionExperimentValueObject

Modifier and Type	Method	Description
Slice<ExpressionExperimentValueObject>	PlatformArgService.getExperiments(PlatformArg<?> arg, int limit, int offset)	Retrieves the Datasets of the Platform that this argument represents.

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

Subclasses of ExpressionExperimentValueObject in ubic.gemma.web.controller.expression.experiment

Modifier and Type	Class	Description
class	ExpressionExperimentEditValueObject

Methods in ubic.gemma.web.controller.expression.experiment that return ExpressionExperimentValueObject

Modifier and Type	Method	Description
ExpressionExperimentValueObject	ExpressionExperimentExperimentalFactorValueObject.getExpressionExperiment()

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

Modifier and Type	Method	Description
Map<ExpressionExperimentValueObject,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.
Collection<ExpressionExperimentValueObject>	ExpressionExperimentController.searchExpressionExperiments(String query)	AJAX (used by ExperimentCombo.js)

Methods in ubic.gemma.web.controller.expression.experiment with parameters of type ExpressionExperimentValueObject

Modifier and Type	Method	Description
void	ExpressionExperimentExperimentalFactorValueObject.setExpressionExperiment(ExpressionExperimentValueObject expressionExperiment)

Constructors in ubic.gemma.web.controller.expression.experiment with parameters of type ExpressionExperimentValueObject

Constructor	Description
ExpressionExperimentEditValueObject(ExpressionExperimentValueObject eevo)

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

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

Modifier and Type	Method	Description
ExpressionExperimentValueObject	VisualizationValueObject.getEevo()