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

Packages that use BioAssaySet

Package	Description
ubic.gemma.core.analysis.expression.coexpression.links
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess.batcheffects
ubic.gemma.core.analysis.service
ubic.gemma.core.apps
ubic.gemma.model.analysis
ubic.gemma.model.analysis.expression
ubic.gemma.model.analysis.expression.coexpression
ubic.gemma.model.association.coexpression
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.analysis
ubic.gemma.persistence.service.analysis.expression
ubic.gemma.persistence.service.analysis.expression.coexpression
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.service.association.coexpression
ubic.gemma.persistence.service.expression.bioAssayData
ubic.gemma.persistence.service.expression.experiment

Uses of BioAssaySet in ubic.gemma.core.analysis.expression.coexpression.links

Methods in ubic.gemma.core.analysis.expression.coexpression.links that return BioAssaySet

Modifier and Type	Method	Description
BioAssaySet	LinkAnalysis.getExpressionExperiment()

Methods in ubic.gemma.core.analysis.expression.coexpression.links with parameters of type BioAssaySet

Modifier and Type	Method	Description
boolean	LinkAnalysisPersister.deleteAnalyses(BioAssaySet ee)	Remove any links and coexpression analyses for the given experiment.
boolean	LinkAnalysisPersisterImpl.deleteAnalyses(BioAssaySet ee)
void	LinkAnalysis.setExpressionExperiment(BioAssaySet expressionExperiment)

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

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

Modifier and Type	Method	Description
Collection<BioAssaySet>	DifferentialExpressionMetaAnalysisValueObject.getActiveExperiments()

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

Modifier and Type	Method	Description
static boolean	DifferentialExpressionAnalysisUtil.blockComplete(BioAssaySet expressionExperiment, Collection<ExperimentalFactor> factors)	Returns true if the block design is complete and there are at least 2 biological replicates for each "group", false otherwise.
static boolean	DifferentialExpressionAnalysisUtil.checkValidForLm(BioAssaySet expressionExperiment, ExperimentalFactor experimentalFactor)	Check that the factorValues are measurements, or that there are at least two assays for at least one factor value.
DifferentialExpressionAnalyzerServiceImpl.AnalysisType	AnalysisSelectionAndExecutionService.determineAnalysis(BioAssaySet bioAssaySet, Collection<ExperimentalFactor> experimentalFactors, ExperimentalFactor subsetFactor, boolean includeInteractions)	Determines the analysis to execute based on the experimental factors, factor values, and block design.
DifferentialExpressionAnalyzerServiceImpl.AnalysisType	AnalysisSelectionAndExecutionService.determineAnalysis(BioAssaySet bioAssaySet, DifferentialExpressionAnalysisConfig config)
DifferentialExpressionAnalyzerServiceImpl.AnalysisType	AnalysisSelectionAndExecutionServiceImpl.determineAnalysis(BioAssaySet bioAssaySet, Collection<ExperimentalFactor> experimentalFactors, ExperimentalFactor subsetFactor, boolean includeInteractionsIfPossible)	FIXME this should probably deal with the case of outliers and also the LinearModelAnalyzer's EXCLUDE_CHARACTERISTICS_VALUES
DifferentialExpressionAnalyzerServiceImpl.AnalysisType	AnalysisSelectionAndExecutionServiceImpl.determineAnalysis(BioAssaySet bioAssaySet, DifferentialExpressionAnalysisConfig config)	FIXME this should probably deal with the case of outliers and also the LinearModelAnalyzer's EXCLUDE_CHARACTERISTICS_VALUES
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, BioAssaySet ee, double threshold, int limit)
static void	LinearModelAnalyzer.populateFactorValuesFromBASet(BioAssaySet ee, ExperimentalFactor f, Collection<FactorValue> fvs)

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

Modifier and Type	Method	Description
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>	GeneDifferentialExpressionServiceImpl.getDifferentialExpression(Gene gene, Collection<BioAssaySet> ees)
DifferentialExpressionMetaAnalysisValueObject	GeneDifferentialExpressionService.getDifferentialExpressionMetaAnalysis(double threshold, Gene g, Map<Long,Long> eeFactorsMap, Collection<BioAssaySet> activeExperiments)	Get the differential expression analysis results for the gene in the activeExperiments.
DifferentialExpressionMetaAnalysisValueObject	GeneDifferentialExpressionServiceImpl.getDifferentialExpressionMetaAnalysis(double threshold, Gene g, Map<Long,Long> eeFactorsMap, Collection<BioAssaySet> activeExperiments)
void	DifferentialExpressionMetaAnalysisValueObject.setActiveExperiments(Collection<BioAssaySet> activeExperiments)

Uses of BioAssaySet in ubic.gemma.core.analysis.preprocess.batcheffects

Methods in ubic.gemma.core.analysis.preprocess.batcheffects that return BioAssaySet

Modifier and Type	Method	Description
BioAssaySet	BatchConfound.getEe()

Methods in ubic.gemma.core.analysis.preprocess.batcheffects with parameters of type BioAssaySet

Modifier and Type	Method	Description
static Collection<BatchConfound>	BatchConfoundUtils.test(BioAssaySet ee)

Constructors in ubic.gemma.core.analysis.preprocess.batcheffects with parameters of type BioAssaySet

Constructor	Description
BatchConfound(BioAssaySet ee, ExperimentalFactor ef, double chiSquare, int df, double p, int numBatches)

Uses of BioAssaySet in ubic.gemma.core.analysis.service

Methods in ubic.gemma.core.analysis.service with parameters of type BioAssaySet

Modifier and Type	Method	Description
void	ExpressionDataFileService.writeDiffExArchiveFile(BioAssaySet ee, DifferentialExpressionAnalysis analysis, DifferentialExpressionAnalysisConfig config)	Writes to the configured gemma.appdata.home The file created is a zip archive containing at least two files.
void	ExpressionDataFileServiceImpl.writeDiffExArchiveFile(BioAssaySet experimentAnalyzed, DifferentialExpressionAnalysis analysis, DifferentialExpressionAnalysisConfig config)

Uses of BioAssaySet in ubic.gemma.core.apps

Fields in ubic.gemma.core.apps with type parameters of type BioAssaySet

Modifier and Type	Field	Description
protected Set<BioAssaySet>	ExpressionExperimentManipulatingCLI.expressionExperiments

Uses of BioAssaySet in ubic.gemma.model.analysis

Methods in ubic.gemma.model.analysis that return BioAssaySet

Modifier and Type	Method	Description
BioAssaySet	SingleExperimentAnalysis.getExperimentAnalyzed()

Methods in ubic.gemma.model.analysis with parameters of type BioAssaySet

Modifier and Type	Method	Description
void	SingleExperimentAnalysis.setExperimentAnalyzed(BioAssaySet experimentAnalyzed)

Constructors in ubic.gemma.model.analysis with parameters of type BioAssaySet

Constructor	Description
SingleExperimentAnalysis(BioAssaySet experimentAnalyzed)

Uses of BioAssaySet in ubic.gemma.model.analysis.expression

Methods in ubic.gemma.model.analysis.expression that return types with arguments of type BioAssaySet

Modifier and Type	Method	Description
Set<BioAssaySet>	ExpressionExperimentSet.getExperiments()

Method parameters in ubic.gemma.model.analysis.expression with type arguments of type BioAssaySet

Modifier and Type	Method	Description
void	ExpressionExperimentSet.setExperiments(Set<BioAssaySet> experiments)

Uses of BioAssaySet in ubic.gemma.model.analysis.expression.coexpression

Constructors in ubic.gemma.model.analysis.expression.coexpression with parameters of type BioAssaySet

Constructor	Description
SampleCoexpressionAnalysis(BioAssaySet experimentAnalyzed, SampleCoexpressionMatrix fullCoexpressionMatrix, SampleCoexpressionMatrix regressedCoexpressionMatrix)

Uses of BioAssaySet in ubic.gemma.model.association.coexpression

Methods in ubic.gemma.model.association.coexpression that return BioAssaySet

Modifier and Type	Method	Description
BioAssaySet	ExperimentCoexpressionLink.getExperiment()

Methods in ubic.gemma.model.association.coexpression with parameters of type BioAssaySet

Modifier and Type	Method	Description
boolean	Gene2GeneCoexpression.isSupportedBy(BioAssaySet bioAssaySet)
void	ExperimentCoexpressionLink.setExperiment(BioAssaySet experiment)

Constructors in ubic.gemma.model.association.coexpression with parameters of type BioAssaySet

Constructor	Description
ExperimentCoexpressionLink(BioAssaySet bioAssaySet, Long linkId, Long firstGene, Long secondGene)
HumanExperimentCoexpressionLinkImpl(BioAssaySet bioAssaySet, Long linkId, Long firstGene, Long secondGene)
MouseExperimentCoexpressionLinkImpl(BioAssaySet bioAssaySet, Long linkId, Long firstGene, Long secondGene)
OtherExperimentCoexpressionLinkImpl(BioAssaySet bioAssaySet, Long linkId, Long firstGene, Long secondGene)
RatExperimentCoexpressionLinkImpl(BioAssaySet bioAssaySet, Long linkId, Long firstGene, Long secondGene)

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

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

Modifier and Type	Class	Description
class	ExpressionExperiment
class	ExpressionExperimentSubSet	A subset of samples from an ExpressionExperiment

Uses of BioAssaySet in ubic.gemma.persistence.service.analysis

Methods in ubic.gemma.persistence.service.analysis that return types with arguments of type BioAssaySet

Modifier and Type	Method	Description
Map<BioAssaySet,Collection<T>>	SingleExperimentAnalysisDao.findByExperiments(Collection<? extends BioAssaySet> experiments)	Given a collection of experiments returns a Map of Analysis --> collection of Experiments The collection of investigations returned by the map will include all the investigations for the analysis key iff one of the investigations for that analysis was in the given collection started with
Map<BioAssaySet,Collection<T>>	SingleExperimentAnalysisDaoBase.findByExperiments(Collection<? extends BioAssaySet> experiments)
Map<BioAssaySet,Collection<T>>	SingleExperimentAnalysisService.findByExperiments(Collection<BioAssaySet> investigations)

Methods in ubic.gemma.persistence.service.analysis with parameters of type BioAssaySet

Modifier and Type	Method	Description
boolean	AnalysisDao.existsByExperiment(BioAssaySet ee)	Indicate if there is an analysis (or at least one) for the given experiment.
boolean	SingleExperimentAnalysisDaoBase.existsByExperiment(BioAssaySet ee)
Collection<T>	SingleExperimentAnalysisDao.findByExperiment(BioAssaySet experiment)	Find by associated experiment via SingleExperimentAnalysis.getExperimentAnalyzed().
Collection<T>	SingleExperimentAnalysisDaoBase.findByExperiment(BioAssaySet experiment)
Collection<T>	SingleExperimentAnalysisService.findByExperiment(BioAssaySet investigation)
void	SingleExperimentAnalysisService.removeForExperiment(BioAssaySet ee)	Removes all analyses for the given experiment

Method parameters in ubic.gemma.persistence.service.analysis with type arguments of type BioAssaySet

Modifier and Type	Method	Description
Map<BioAssaySet,Collection<T>>	SingleExperimentAnalysisDao.findByExperiments(Collection<? extends BioAssaySet> experiments)	Given a collection of experiments returns a Map of Analysis --> collection of Experiments The collection of investigations returned by the map will include all the investigations for the analysis key iff one of the investigations for that analysis was in the given collection started with
Map<BioAssaySet,Collection<T>>	SingleExperimentAnalysisDaoBase.findByExperiments(Collection<? extends BioAssaySet> experiments)
Map<BioAssaySet,Collection<T>>	SingleExperimentAnalysisService.findByExperiments(Collection<BioAssaySet> investigations)

Uses of BioAssaySet in ubic.gemma.persistence.service.analysis.expression

Methods in ubic.gemma.persistence.service.analysis.expression with parameters of type BioAssaySet

Modifier and Type	Method	Description
Collection<ExpressionExperimentSet>	ExpressionExperimentSetDao.find(BioAssaySet bioAssaySet)
Collection<ExpressionExperimentSet>	ExpressionExperimentSetDaoImpl.find(BioAssaySet bioAssaySet)

Uses of BioAssaySet in ubic.gemma.persistence.service.analysis.expression.coexpression

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

Modifier and Type	Method	Description
Map<BioAssaySet,Collection<CoexpressionAnalysis>>	CoexpressionAnalysisServiceImpl.findByExperiments(Collection<BioAssaySet> investigations)

Methods in ubic.gemma.persistence.service.analysis.expression.coexpression with parameters of type BioAssaySet

Modifier and Type	Method	Description
Collection<CoexpressionAnalysis>	CoexpressionAnalysisServiceImpl.findByExperiment(BioAssaySet investigation)
void	CoexpressionAnalysisService.removeForExperiment(BioAssaySet ee)
void	CoexpressionAnalysisServiceImpl.removeForExperiment(BioAssaySet ee)

Method parameters in ubic.gemma.persistence.service.analysis.expression.coexpression with type arguments of type BioAssaySet

Modifier and Type	Method	Description
Map<BioAssaySet,Collection<CoexpressionAnalysis>>	CoexpressionAnalysisServiceImpl.findByExperiments(Collection<BioAssaySet> investigations)

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

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

Modifier and Type	Method	Description
Map<BioAssaySet,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisServiceImpl.findByExperiments(Collection<BioAssaySet> experiments)
Map<BioAssaySet,Collection<GeneDifferentialExpressionMetaAnalysis>>	GeneDiffExMetaAnalysisDao.findByExperiments(Collection<? extends BioAssaySet> experiments)
Map<BioAssaySet,Collection<GeneDifferentialExpressionMetaAnalysis>>	GeneDiffExMetaAnalysisDaoImpl.findByExperiments(Collection<? extends BioAssaySet> experiments)
Collection<BioAssaySet>	DifferentialExpressionAnalysisDao.findExperimentsWithAnalyses(Gene gene)
Collection<BioAssaySet>	DifferentialExpressionAnalysisService.findExperimentsWithAnalyses(Gene gene)
Collection<BioAssaySet>	DifferentialExpressionAnalysisServiceImpl.findExperimentsWithAnalyses(Gene gene)

Methods in ubic.gemma.persistence.service.analysis.expression.diff with parameters of type BioAssaySet

Modifier and Type	Method	Description
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisServiceImpl.findByExperiment(BioAssaySet experiment)
Collection<GeneDifferentialExpressionMetaAnalysis>	GeneDiffExMetaAnalysisDao.findByExperiment(BioAssaySet experiment)
Collection<GeneDifferentialExpressionMetaAnalysis>	GeneDiffExMetaAnalysisDaoImpl.findByExperiment(BioAssaySet experiment)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisService.getAnalyses(BioAssaySet expressionExperiment)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisServiceImpl.getAnalyses(BioAssaySet expressionExperiment)
void	DifferentialExpressionAnalysisServiceImpl.removeForExperiment(BioAssaySet ee)
void	GeneDiffExMetaAnalysisDao.removeForExperiment(BioAssaySet ee)
void	GeneDiffExMetaAnalysisDaoImpl.removeForExperiment(BioAssaySet ee)

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

Modifier and Type	Method	Description
Slice<DifferentialExpressionAnalysisResultSetValueObject>	ExpressionAnalysisResultSetDao.findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> databaseEntries, Filters filters, int offset, int limit, Sort sort)	Retrieve result sets associated to a set of BioAssaySet and external database entries.
Slice<DifferentialExpressionAnalysisResultSetValueObject>	ExpressionAnalysisResultSetDaoImpl.findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> databaseEntries, Filters filters, int offset, int limit, Sort sort)
Slice<DifferentialExpressionAnalysisResultSetValueObject>	ExpressionAnalysisResultSetService.findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> externalIds, Filters filters, int offset, int limit, Sort sort)
Slice<DifferentialExpressionAnalysisResultSetValueObject>	ExpressionAnalysisResultSetServiceImpl.findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> externalIds, Filters filters, int offset, int limit, Sort sort)
Map<BioAssaySet,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisServiceImpl.findByExperiments(Collection<BioAssaySet> experiments)
Map<BioAssaySet,Collection<GeneDifferentialExpressionMetaAnalysis>>	GeneDiffExMetaAnalysisDao.findByExperiments(Collection<? extends BioAssaySet> experiments)
Map<BioAssaySet,Collection<GeneDifferentialExpressionMetaAnalysis>>	GeneDiffExMetaAnalysisDaoImpl.findByExperiments(Collection<? extends BioAssaySet> experiments)
Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisDao.getAnalyses(Collection<? extends BioAssaySet> expressionExperiments)
Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisService.getAnalyses(Collection<? extends BioAssaySet> expressionExperiments)
Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisServiceImpl.getAnalyses(Collection<? extends BioAssaySet> expressionExperiments)

Uses of BioAssaySet in ubic.gemma.persistence.service.association.coexpression

Methods in ubic.gemma.persistence.service.association.coexpression with parameters of type BioAssaySet

Modifier and Type	Method	Description
Integer	CoexpressionDao.countLinks(Gene gene, BioAssaySet ee)
Integer	CoexpressionDaoImpl.countLinks(Gene gene, BioAssaySet ee)
Integer	CoexpressionService.countLinks(BioAssaySet ee, Gene gene)
Integer	CoexpressionServiceImpl.countLinks(BioAssaySet ee, Gene gene)
ExperimentCoexpressionLink	LinkCreator.createEELink(BioAssaySet bas, Long linkid, Long firstGene, Long secondGene)
void	CoexpressionDao.createOrUpdate(BioAssaySet bioAssaySet, List<NonPersistentNonOrderedCoexpLink> p2plinks, LinkCreator c, Set<Gene> genesTested)
void	CoexpressionDaoImpl.createOrUpdate(BioAssaySet bioAssaySet, List<NonPersistentNonOrderedCoexpLink> links, LinkCreator c, Set<Gene> genesTested)
void	CoexpressionService.createOrUpdate(BioAssaySet bioAssaySet, List<NonPersistentNonOrderedCoexpLink> links, LinkCreator c, Set<Gene> geesTested)	Maintenance method.
void	CoexpressionServiceImpl.createOrUpdate(BioAssaySet bioAssaySet, List<NonPersistentNonOrderedCoexpLink> links, LinkCreator c, Set<Gene> genesTested)
void	CoexpressionDao.deleteLinks(Taxon taxon, BioAssaySet experiment)
void	CoexpressionDaoImpl.deleteLinks(Taxon t, BioAssaySet experiment)
void	CoexpressionService.deleteLinks(BioAssaySet experiment)	Maintenance method.
void	CoexpressionServiceImpl.deleteLinks(BioAssaySet experiment)
Collection<CoexpressionValueObject>	CoexpressionDao.getCoexpression(Taxon taxon, BioAssaySet experiment, boolean quick)
Collection<CoexpressionValueObject>	CoexpressionDaoImpl.getCoexpression(Taxon taxon, BioAssaySet experiment, boolean quick)
Collection<CoexpressionValueObject>	CoexpressionService.getCoexpression(BioAssaySet experiment, boolean quick)
Collection<CoexpressionValueObject>	CoexpressionServiceImpl.getCoexpression(BioAssaySet experiment, boolean quick)
boolean	CoexpressionDao.hasLinks(Taxon taxon, BioAssaySet ee)
boolean	CoexpressionDaoImpl.hasLinks(Taxon taxon, BioAssaySet ee)
boolean	CoexpressionService.hasLinks(BioAssaySet ee)	Check if a given dataset has coexpression links.
boolean	CoexpressionServiceImpl.hasLinks(BioAssaySet ee)
void	CoexpressionDaoImpl.updateModifiedSupportDetails(BioAssaySet experiment, Collection<SupportDetails> supportDetailsToDelete, Collection<SupportDetails> supportDetailsToUpdate)

Uses of BioAssaySet in ubic.gemma.persistence.service.expression.bioAssayData

Methods in ubic.gemma.persistence.service.expression.bioAssayData with parameters of type BioAssaySet

Modifier and Type	Method	Description
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorService.getProcessedDataArrays(BioAssaySet expressionExperiment)	Retrieve processed vectors for a given experiment or subset.
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorService.getProcessedDataArrays(BioAssaySet expressionExperiment, Collection<Long> genes)	Retrieve processed vectors by genes for a given experiment or subset.
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorServiceImpl.getProcessedDataArrays(BioAssaySet expressionExperiment)
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorServiceImpl.getProcessedDataArrays(BioAssaySet expressionExperiment, Collection<Long> genes)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorService.getProcessedDataArrays(BioAssaySet bioAssaySet, Collection<Long> genes)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataArrays(BioAssaySet bioAssaySet, Collection<Long> genes)
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorService.getProcessedDataArraysByProbeIds(BioAssaySet ee, Collection<Long> probes)
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorServiceImpl.getProcessedDataArraysByProbeIds(BioAssaySet ee, Collection<Long> probes)
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorService.getRandomProcessedDataArrays(BioAssaySet expressionExperiment, int limit)	Retrieve random processed vectors for a given experiment or subset.
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorServiceImpl.getRandomProcessedDataArrays(BioAssaySet ee, int limit)

Method parameters in ubic.gemma.persistence.service.expression.bioAssayData with type arguments of type BioAssaySet

Modifier and Type	Method	Description
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorService.getProcessedDataArrays(Collection<? extends BioAssaySet> expressionExperiments, Collection<Long> genes)	Retrieve processed vectors by genes and experiments.
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorServiceImpl.getProcessedDataArrays(Collection<? extends BioAssaySet> expressionExperiments, Collection<Long> genes)
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorService.getProcessedDataArraysByProbe(Collection<? extends BioAssaySet> expressionExperiments, Collection<CompositeSequence> probes)	Retrieves processed vectors by probes and experiments
Collection<DoubleVectorValueObject>	CachedProcessedExpressionDataVectorServiceImpl.getProcessedDataArraysByProbe(Collection<? extends BioAssaySet> ees, Collection<CompositeSequence> probes)

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

Methods in ubic.gemma.persistence.service.expression.experiment with type parameters of type BioAssaySet

Modifier and Type	Method	Description
<T extends BioAssaySet> Map<T,Taxon>	ExpressionExperimentDao.getTaxa(Collection<T> bioAssaySets)
<T extends BioAssaySet> Map<T,Taxon>	ExpressionExperimentDaoImpl.getTaxa(Collection<T> bioAssaySets)
<T extends BioAssaySet> Map<T,Taxon>	ExpressionExperimentService.getTaxa(Collection<T> bioAssaySets)	Return the taxon for each of the given experiments (or subsets).
<T extends BioAssaySet> Map<T,Taxon>	ExpressionExperimentServiceImpl.getTaxa(Collection<T> bioAssaySets)

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

Modifier and Type	Method	Description
BioAssaySet	BioAssaySetServiceImpl.find(BioAssaySet entity)
BioAssaySet	BioAssaySetServiceImpl.findOrFail(BioAssaySet entity)
BioAssaySet	BioAssaySetServiceImpl.load(Long id)
BioAssaySet	ExpressionExperimentDao.loadBioAssaySet(Long id)
BioAssaySet	ExpressionExperimentDaoImpl.loadBioAssaySet(Long id)
BioAssaySet	ExpressionExperimentService.loadBioAssaySet(Long id)	Load a BioAssaySet by ID which can be either a ExpressionExperiment or a ExpressionExperimentSubSet.
BioAssaySet	ExpressionExperimentServiceImpl.loadBioAssaySet(Long id)
BioAssaySet	BioAssaySetServiceImpl.loadOrFail(Long id)
<T extends Exception> BioAssaySet	BioAssaySetServiceImpl.loadOrFail(Long id, Function<String,T> exceptionSupplier)
<T extends Exception> BioAssaySet	BioAssaySetServiceImpl.loadOrFail(Long id, Function<String,T> exceptionSupplier, String message)
<T extends Exception> BioAssaySet	BioAssaySetServiceImpl.loadOrFail(Long id, Supplier<T> exceptionSupplier)

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

Modifier and Type	Method	Description
Class<? extends BioAssaySet>	BioAssaySetServiceImpl.getElementClass()
Collection<BioAssaySet>	BioAssaySetServiceImpl.load(Collection<Long> ids)
Collection<BioAssaySet>	BioAssaySetServiceImpl.loadAll()

Methods in ubic.gemma.persistence.service.expression.experiment with parameters of type BioAssaySet

Modifier and Type	Method	Description
BioAssaySet	BioAssaySetServiceImpl.find(BioAssaySet entity)
Collection<ExpressionExperimentSet>	ExpressionExperimentSetService.find(BioAssaySet bioAssaySet)
Collection<ExpressionExperimentSet>	ExpressionExperimentSetServiceImpl.find(BioAssaySet bioAssaySet)
Collection<Long>	ExpressionExperimentSetService.findIds(BioAssaySet bioAssaySet)	security at DAO level
Collection<Long>	ExpressionExperimentSetServiceImpl.findIds(BioAssaySet bioAssaySet)
BioAssaySet	BioAssaySetServiceImpl.findOrFail(BioAssaySet entity)
Collection<ArrayDesign>	ExpressionExperimentDao.getArrayDesignsUsed(BioAssaySet bas)
Collection<ArrayDesign>	ExpressionExperimentDaoImpl.getArrayDesignsUsed(BioAssaySet bas)
Collection<ArrayDesign>	ExpressionExperimentService.getArrayDesignsUsed(BioAssaySet expressionExperiment)
Collection<ArrayDesign>	ExpressionExperimentServiceImpl.getArrayDesignsUsed(BioAssaySet expressionExperiment)
Taxon	ExpressionExperimentDao.getTaxon(BioAssaySet ee)	Determine the taxon for a given experiment or subset.
Taxon	ExpressionExperimentDaoImpl.getTaxon(BioAssaySet ee)
Taxon	ExpressionExperimentService.getTaxon(BioAssaySet bioAssaySet)	Returns the taxon of the given experiment or subset.
Taxon	ExpressionExperimentServiceImpl.getTaxon(BioAssaySet bioAssaySet)
void	BioAssaySetService.remove(BioAssaySet entity)
void	BioAssaySetServiceImpl.remove(BioAssaySet entity)
int	ExpressionExperimentSetService.removeFromSets(BioAssaySet bas)	Remove an experiment from all sets it is in.
int	ExpressionExperimentSetServiceImpl.removeFromSets(BioAssaySet bas)

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

Modifier and Type	Method	Description
void	BioAssaySetService.remove(Collection<? extends BioAssaySet> entities)
void	BioAssaySetServiceImpl.remove(Collection<? extends BioAssaySet> entities)