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

Packages that use BioAssaySet

Package	Description
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess.batcheffects
ubic.gemma.core.loader.util.mapper	Utilities for mapping Identifiable entities to external identifiers.
ubic.gemma.core.visualization
ubic.gemma.model.analysis
ubic.gemma.model.analysis.expression.diff
ubic.gemma.model.expression.bioAssay
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.service.expression.bioAssay
ubic.gemma.persistence.service.expression.bioAssayData
ubic.gemma.persistence.util

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.
static AnalysisType	DiffExAnalyzerUtils.determineAnalysisType(BioAssaySet bioAssaySet, Collection<ExperimentalFactor> experimentalFactors, ExperimentalFactor subsetFactor, boolean includeInteractionsIfPossible)	Determines the analysis to execute based on the experimental factors, factor values, and block design.
static AnalysisType	DiffExAnalyzerUtils.determineAnalysisType(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 experimentAnalyzed, boolean includeSubSets, 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 experimentAnalyzed, boolean includeSubSets, double threshold, int limit)
static void	DiffExAnalyzerUtils.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> experimentsAnalyzed, boolean includeSubSets)	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> experimentsAnalyzed, boolean includeSubSets)
DifferentialExpressionMetaAnalysisValueObject	GeneDifferentialExpressionService.getDifferentialExpressionMetaAnalysis(double threshold, Gene g, Map<Long,Long> eeFactorsMap, Collection<BioAssaySet> activeExperiments, boolean includeSubSets)	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> experimentsAnalyzed, boolean includeSubSets)
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.getBioAssaySet()	Experiment or subset this confound is applicable to.

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

Modifier	Constructor	Description
	BatchConfound(BioAssaySet bioAssaySet, ExperimentalFactor factor, double chiSquare, int df, double pValue, int numBatches)	Creates a new BatchConfound instance.

Uses of BioAssaySet in ubic.gemma.core.loader.util.mapper

Methods in ubic.gemma.core.loader.util.mapper with parameters of type BioAssaySet

Modifier and Type	Method	Description
default EntityMapper.StatefulEntityMapper<BioAssay>	BioAssayMapper.forCandidates(BioAssaySet bioAssaySet)

Uses of BioAssaySet in ubic.gemma.core.visualization

Methods in ubic.gemma.core.visualization that return BioAssaySet

Modifier and Type	Method	Description
BioAssaySet	ExpressionDataHeatmap.getBioAssaySet()

Uses of BioAssaySet in ubic.gemma.model.analysis

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

Modifier and Type	Class	Description
class	SingleExperimentAnalysis<T extends BioAssaySet>	An analysis of a single experiment or subset.

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

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

Modifier and Type	Method	Description
static DifferentialExpressionAnalysis	RandomDifferentialExpressionAnalysisUtils.randomAnalysis(BioAssaySet experimentAnalyzed, ExperimentalDesign design, ArrayDesign platform)

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

Methods in ubic.gemma.model.expression.bioAssay with parameters of type BioAssaySet

Modifier and Type	Method	Description
static Map<BioAssay,BioAssay>	BioAssayUtils.createBioAssayToSourceBioAssayMap(BioAssaySet sourceAssaySet, Collection<BioAssay> bas)	Create a mapping between assays and their source assays from a given BioAssaySet.

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.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,List<DifferentialExpressionAnalysisResult>>	DifferentialExpressionResultDao.findByExperimentAnalyzed(Collection<Long> experimentAnalyzedIds, boolean includeSubSets, 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<BioAssaySet,List<DifferentialExpressionAnalysisResult>>	DifferentialExpressionResultDaoImpl.findByExperimentAnalyzed(Collection<Long> experimentAnalyzedIds, boolean includeSubSets, double threshold, int limit)
Map<BioAssaySet,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisService.findByExperiments(Collection<ExpressionExperiment> investigations, boolean includeSubSets)
Map<BioAssaySet,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisServiceImpl.findByExperiments(Collection<ExpressionExperiment> experiments, boolean includeSubSets)
Map<BioAssaySet,Collection<GeneDifferentialExpressionMetaAnalysis>>	GeneDiffExMetaAnalysisDao.findByExperiments(Collection<? extends BioAssaySet> experiments)
Map<BioAssaySet,Collection<GeneDifferentialExpressionMetaAnalysis>>	GeneDiffExMetaAnalysisDaoImpl.findByExperiments(Collection<? extends BioAssaySet> experiments)
Map<BioAssaySet,Collection<DifferentialExpressionAnalysis>>	DifferentialExpressionAnalysisDao.findByExperimentsAnalyzed(Collection<ExpressionExperiment> experiments, boolean includeSubSets)	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,List<DifferentialExpressionAnalysisResult>>	DifferentialExpressionResultDao.findByGene(Gene gene, boolean keepNonSpecificProbes)	Find differential expression results for a given gene, grouped by experiment.
Map<BioAssaySet,List<DifferentialExpressionAnalysisResult>>	DifferentialExpressionResultDao.findByGene(Gene gene, boolean keepNonSpecificProbes, double threshold, int limit)	Find differential expression for a gene, exceeding a given significance level (using the corrected pvalue field)
Map<BioAssaySet,List<DifferentialExpressionAnalysisResult>>	DifferentialExpressionResultDaoImpl.findByGene(Gene gene, boolean keepNonSpecificProbes)
Map<BioAssaySet,List<DifferentialExpressionAnalysisResult>>	DifferentialExpressionResultDaoImpl.findByGene(Gene gene, boolean keepNonSpecificProbes, double threshold, int limit)
Map<BioAssaySet,List<DifferentialExpressionAnalysisResult>>	DifferentialExpressionResultDao.findByGeneAndExperimentAnalyzed(Gene gene, boolean keepNonSpecificProbes, Collection<Long> experimentAnalyzedIds, boolean includeSubSets)	Find differential expression results for a given gene and set of experiments, grouped by experiment.
Map<BioAssaySet,List<DifferentialExpressionAnalysisResult>>	DifferentialExpressionResultDao.findByGeneAndExperimentAnalyzed(Gene gene, boolean keepNonSpecificProbes, Collection<Long> experimentsAnalyzed, boolean includeSubSets, 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<BioAssaySet,List<DifferentialExpressionAnalysisResult>>	DifferentialExpressionResultDaoImpl.findByGeneAndExperimentAnalyzed(Gene gene, boolean keepNonSpecificProbes, Collection<Long> experimentAnalyzedIds, boolean includeSubSets)
Map<BioAssaySet,List<DifferentialExpressionAnalysisResult>>	DifferentialExpressionResultDaoImpl.findByGeneAndExperimentAnalyzed(Gene gene, boolean keepNonSpecificProbes, Collection<Long> experimentAnalyzedIds, boolean includeSubsets, double threshold, int limit)
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<GeneDifferentialExpressionMetaAnalysis>	GeneDiffExMetaAnalysisDao.findByExperiment(BioAssaySet experiment)
Collection<GeneDifferentialExpressionMetaAnalysis>	GeneDiffExMetaAnalysisDaoImpl.findByExperiment(BioAssaySet experiment)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisDao.findByExperimentAnalyzed(BioAssaySet experimentAnalyzed)
void	GeneDiffExMetaAnalysisDao.removeForExperiment(BioAssaySet ee)
void	GeneDiffExMetaAnalysisDaoImpl.removeForExperiment(BioAssaySet ee)
void	DifferentialExpressionAnalysisService.removeForExperimentAnalyzed(BioAssaySet experimentAnalyzed)
void	DifferentialExpressionAnalysisServiceImpl.removeForExperimentAnalyzed(BioAssaySet experimentAnalyzed)

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<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultService.findByExperimentAnalyzed(Collection<? extends BioAssaySet> experimentsAnalyzed, boolean includeSubSets, 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>>	DifferentialExpressionResultServiceImpl.findByExperimentAnalyzed(Collection<? extends BioAssaySet> experimentsAnalyzed, boolean includeSubSets, double threshold, int limit)
Map<BioAssaySet,Collection<GeneDifferentialExpressionMetaAnalysis>>	GeneDiffExMetaAnalysisDao.findByExperiments(Collection<? extends BioAssaySet> experiments)
Map<BioAssaySet,Collection<GeneDifferentialExpressionMetaAnalysis>>	GeneDiffExMetaAnalysisDaoImpl.findByExperiments(Collection<? extends BioAssaySet> experiments)
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultService.findByGeneAndExperimentAnalyzed(Gene gene, boolean keepNonSpecificProbes, Collection<? extends BioAssaySet> experimentsAnalyzed, boolean includeSubSets)	Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultService.findByGeneAndExperimentAnalyzed(Gene gene, boolean keepNonSpecificProbes, Collection<? extends BioAssaySet> experimentsAnalyzed, boolean includeSubSets, 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.findByGeneAndExperimentAnalyzed(Gene gene, boolean keepNonSpecificProbes, Collection<? extends BioAssaySet> experimentsAnalyzed, boolean includeSubSets)
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultServiceImpl.findByGeneAndExperimentAnalyzed(Gene gene, boolean keepNonSpecificProbes, Collection<? extends BioAssaySet> experimentsAnalyzed, boolean includeSubSets, double threshold, int limit)

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

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

Modifier and Type	Method	Description
Collection<BioAssaySet>	BioAssayDao.getBioAssaySets(BioAssay bioAssay)
Collection<BioAssaySet>	BioAssayDaoImpl.getBioAssaySets(BioAssay bioAssay)
Collection<BioAssaySet>	BioAssayService.getBioAssaySets(BioAssay bioAssay)	Obtain all the BioAssaySet that contain the given BioAssay.
Collection<BioAssaySet>	BioAssayServiceImpl.getBioAssaySets(BioAssay bioAssay)

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>	ProcessedExpressionDataVectorService.getProcessedDataArrays(BioAssaySet bioAssaySet, Collection<Long> genes)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataArrays(BioAssaySet bioAssaySet, Collection<Long> genes)

Uses of BioAssaySet in ubic.gemma.persistence.util

Methods in ubic.gemma.persistence.util with parameters of type BioAssaySet

Modifier and Type	Method	Description
static Collection<ArrayDesign>	CommonQueries.getArrayDesignsUsed(BioAssaySet bas, Session session)	Retrieve a list of array designs used in given expression experiment

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

Modifier and Type	Method	Description
static Collection<ArrayDesign>	CommonQueries.getArrayDesignsUsed(Collection<? extends BioAssaySet> ees, Session session)	Retrieve a list of array designs used by the given experiments.