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

Packages that use ExperimentalFactor

Package	Description
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess
ubic.gemma.core.analysis.preprocess.batcheffects
ubic.gemma.core.analysis.preprocess.svd
ubic.gemma.core.analysis.util
ubic.gemma.core.datastructure.matrix
ubic.gemma.core.tasks.analysis.diffex
ubic.gemma.core.visualization
ubic.gemma.model.analysis.expression
ubic.gemma.model.analysis.expression.diff
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util
ubic.gemma.web.controller.expression.experiment
ubic.gemma.web.controller.visualization

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

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

Modifier and Type	Method	Description
ExperimentalFactor	DiffExAnalyzer.determineInterceptFactor(Collection<ExperimentalFactor> factors, QuantitationType quantitationType)
ExperimentalFactor	LinearModelAnalyzer.determineInterceptFactor(Collection<ExperimentalFactor> factors, QuantitationType quantitationType)	Determine if any factor should be treated as the intercept term.
ExperimentalFactor	DifferentialExpressionAnalysisConfig.getSubsetFactor()

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

Modifier and Type	Method	Description
Map<ExperimentalFactor,FactorValue>	DifferentialExpressionAnalysisConfig.getBaseLineFactorValues()
List<ExperimentalFactor>	DifferentialExpressionAnalysisConfig.getFactorsToInclude()
Collection<Collection<ExperimentalFactor>>	DifferentialExpressionAnalysisConfig.getInteractionsToInclude()

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

Modifier and Type	Method	Description
void	DifferentialExpressionAnalysisConfig.addInteractionToInclude(ExperimentalFactor... factors)
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.
ExperimentalFactorValueObject	GeneDifferentialExpressionService.configExperimentalFactorValueObject(ExperimentalFactor ef)
ExperimentalFactorValueObject	GeneDifferentialExpressionServiceImpl.configExperimentalFactorValueObject(ExperimentalFactor ef)
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	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
static void	LinearModelAnalyzer.populateFactorValuesFromBASet(BioAssaySet ee, ExperimentalFactor f, Collection<FactorValue> fvs)
void	DifferentialExpressionAnalysisConfig.setSubsetFactor(ExperimentalFactor subsetFactor)

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

Modifier and Type	Method	Description
void	DifferentialExpressionAnalysisConfig.addInteractionToInclude(Collection<ExperimentalFactor> factors)
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.
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	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
ExperimentalFactor	DiffExAnalyzer.determineInterceptFactor(Collection<ExperimentalFactor> factors, QuantitationType quantitationType)
ExperimentalFactor	LinearModelAnalyzer.determineInterceptFactor(Collection<ExperimentalFactor> factors, QuantitationType quantitationType)	Determine if any factor should be treated as the intercept term.
void	DifferentialExpressionAnalysisConfig.setBaseLineFactorValues(Map<ExperimentalFactor,FactorValue> baseLineFactorValues)
void	DifferentialExpressionAnalysisConfig.setFactorsToInclude(Collection<ExperimentalFactor> factorsToInclude)
void	DifferentialExpressionAnalysisConfig.setFactorsToInclude(List<ExperimentalFactor> factorsToInclude)
void	DifferentialExpressionAnalysisConfig.setInteractionsToInclude(Collection<Collection<ExperimentalFactor>> interactionsToInclude)

Uses of ExperimentalFactor in ubic.gemma.core.analysis.preprocess

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

Modifier and Type	Method	Description
ExpressionExperimentSet	SplitExperimentService.split(ExpressionExperiment expressionExperiment, ExperimentalFactor splitOn, boolean postProcess)	Split an experiment into multiple experiments based on a factor.
ExpressionExperimentSet	SplitExperimentServiceImpl.split(ExpressionExperiment toSplit, ExperimentalFactor splitOn, boolean postProcess)

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

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

Modifier and Type	Method	Description
ExperimentalFactor	BatchInfoPopulationHelperService.createBatchFactor(ExpressionExperiment ee, Map<BioMaterial,Date> dates)
ExperimentalFactor	BatchInfoPopulationHelperServiceImpl.createBatchFactor(ExpressionExperiment ee, Map<BioMaterial,Date> dates)
ExperimentalFactor	BatchInfoPopulationHelperService.createRnaSeqBatchFactor(ExpressionExperiment ee, Map<BioMaterial,String> headers)	For RNA-seq, we based the batching on the available device/run/flowcell/lane information
ExperimentalFactor	BatchInfoPopulationHelperServiceImpl.createRnaSeqBatchFactor(ExpressionExperiment ee, Map<BioMaterial,String> headers)
ExperimentalFactor	ExpressionExperimentBatchCorrectionService.getBatchFactor(ExpressionExperiment ee)	For convenience of some testing classes
ExperimentalFactor	ExpressionExperimentBatchCorrectionServiceImpl.getBatchFactor(ExpressionExperiment ee)
ExperimentalFactor	BatchConfound.getEf()

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

Modifier and Type	Method	Description
static boolean	BatchInfoPopulationServiceImpl.isBatchFactor(ExperimentalFactor ef)

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

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

Uses of ExperimentalFactor in ubic.gemma.core.analysis.preprocess.svd

Methods in ubic.gemma.core.analysis.preprocess.svd that return types with arguments of type ExperimentalFactor

Modifier and Type	Method	Description
Set<ExperimentalFactor>	SVDServiceHelper.getImportantFactors(ExpressionExperiment ee, Collection<ExperimentalFactor> experimentalFactors, Double importanceThreshold)
Set<ExperimentalFactor>	SVDServiceHelperImpl.getImportantFactors(ExpressionExperiment ee, Collection<ExperimentalFactor> experimentalFactors, Double importanceThreshold)

Methods in ubic.gemma.core.analysis.preprocess.svd with parameters of type ExperimentalFactor

Modifier and Type	Method	Description
void	SVDValueObject.setPCFactorCorrelation(int componentNumber, ExperimentalFactor ef, double factorCorrelation)
void	SVDValueObject.setPCFactorCorrelationPval(int componentNumber, ExperimentalFactor ef, double pvalue)

Method parameters in ubic.gemma.core.analysis.preprocess.svd with type arguments of type ExperimentalFactor

Modifier and Type	Method	Description
Set<ExperimentalFactor>	SVDServiceHelper.getImportantFactors(ExpressionExperiment ee, Collection<ExperimentalFactor> experimentalFactors, Double importanceThreshold)
Set<ExperimentalFactor>	SVDServiceHelperImpl.getImportantFactors(ExpressionExperiment ee, Collection<ExperimentalFactor> experimentalFactors, Double importanceThreshold)
static void	SVDServiceHelperImpl.populateBMFMap(Map<ExperimentalFactor,Map<Long,Double>> bioMaterialFactorMap, BioMaterial bm)	Retrieve relationships between factors, biomaterials and factor values.

Uses of ExperimentalFactor in ubic.gemma.core.analysis.util

Methods in ubic.gemma.core.analysis.util that return types with arguments of type ExperimentalFactor

Modifier and Type	Method	Description
static Collection<ExperimentalFactor>	ExperimentalDesignUtils.factorsWithoutBatch(Collection<ExperimentalFactor> factors)
static Map<ExperimentalFactor,FactorValue>	ExperimentalDesignUtils.getBaselineConditions(List<BioMaterial> samplesUsed, List<ExperimentalFactor> factors)
static ObjectMatrix<BioMaterial,ExperimentalFactor,Object>	ExperimentalDesignUtils.sampleInfoMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, Map<ExperimentalFactor,FactorValue> baselines)
static List<ExperimentalFactor>	ExperimentalDesignUtils.sortFactors(Collection<ExperimentalFactor> factors)	Sort factors in a consistent way.

Methods in ubic.gemma.core.analysis.util with parameters of type ExperimentalFactor

Modifier and Type	Method	Description
static boolean	ExperimentalDesignUtils.isBatch(ExperimentalFactor ef)
static boolean	ExperimentalDesignUtils.isComplete(ExperimentalFactor factor, List<BioMaterial> samplesUsed, Map<ExperimentalFactor,FactorValue> baselines)	Check if a factor has missing values (samples that lack an assigned value)
static boolean	ExperimentalDesignUtils.isContinuous(ExperimentalFactor ef)
static String	ExperimentalDesignUtils.nameForR(ExperimentalFactor experimentalFactor)

Method parameters in ubic.gemma.core.analysis.util with type arguments of type ExperimentalFactor

Modifier and Type	Method	Description
static ObjectMatrix<String,String,Object>	ExperimentalDesignUtils.buildDesignMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, Map<ExperimentalFactor,FactorValue> baselines)	Convert factors to a matrix usable in R.
static ObjectMatrix<String,String,Object>	ExperimentalDesignUtils.buildDesignMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, Map<ExperimentalFactor,FactorValue> baselines)	Convert factors to a matrix usable in R.
static Collection<ExperimentalFactor>	ExperimentalDesignUtils.factorsWithoutBatch(Collection<ExperimentalFactor> factors)
static List<BioMaterial>	ExperimentalDesignUtils.getOrderedSamples(ExpressionDataDoubleMatrix dmatrix, List<ExperimentalFactor> factors)	This puts the control samples up front if possible.
static boolean	ExperimentalDesignUtils.isComplete(ExperimentalFactor factor, List<BioMaterial> samplesUsed, Map<ExperimentalFactor,FactorValue> baselines)	Check if a factor has missing values (samples that lack an assigned value)
static ObjectMatrix<BioMaterial,ExperimentalFactor,Object>	ExperimentalDesignUtils.sampleInfoMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, Map<ExperimentalFactor,FactorValue> baselines)
static ObjectMatrix<BioMaterial,ExperimentalFactor,Object>	ExperimentalDesignUtils.sampleInfoMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, Map<ExperimentalFactor,FactorValue> baselines)
static List<ExperimentalFactor>	ExperimentalDesignUtils.sortFactors(Collection<ExperimentalFactor> factors)	Sort factors in a consistent way.

Uses of ExperimentalFactor in ubic.gemma.core.datastructure.matrix

Methods in ubic.gemma.core.datastructure.matrix that return types with arguments of type ExperimentalFactor

Modifier and Type	Method	Description
static Map<ExperimentalFactor,FactorValue>	ExpressionDataMatrixColumnSort.getBaselineLevels(Collection<ExperimentalFactor> factors)	Identify the FactorValue that should be treated as 'Baseline' for each of the given factors.
static Map<ExperimentalFactor,FactorValue>	ExpressionDataMatrixColumnSort.getBaselineLevels(List<BioMaterial> samplesUsed, Collection<ExperimentalFactor> factors)	Identify the FactorValue that should be treated as 'Baseline' for each of the given factors.

Methods in ubic.gemma.core.datastructure.matrix with parameters of type ExperimentalFactor

Modifier and Type	Method	Description
static List<BioMaterial>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(List<BioMaterial> start, Collection<ExperimentalFactor> factors, ExperimentalFactor primaryFactor)
static <R> DoubleMatrix<R,BioAssay>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(DoubleMatrix<R,BioAssay> mat, ExperimentalFactor primaryFactor)
static List<BioMaterial>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(ExpressionDataMatrix<?> mat, ExperimentalFactor primaryFactor)

Method parameters in ubic.gemma.core.datastructure.matrix with type arguments of type ExperimentalFactor

Modifier and Type	Method	Description
static Map<ExperimentalFactor,FactorValue>	ExpressionDataMatrixColumnSort.getBaselineLevels(Collection<ExperimentalFactor> factors)	Identify the FactorValue that should be treated as 'Baseline' for each of the given factors.
static Map<ExperimentalFactor,FactorValue>	ExpressionDataMatrixColumnSort.getBaselineLevels(List<BioMaterial> samplesUsed, Collection<ExperimentalFactor> factors)	Identify the FactorValue that should be treated as 'Baseline' for each of the given factors.
static List<BioMaterial>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(List<BioMaterial> start, Collection<ExperimentalFactor> factors)
static List<BioMaterial>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(List<BioMaterial> start, Collection<ExperimentalFactor> factors, ExperimentalFactor primaryFactor)

Uses of ExperimentalFactor in ubic.gemma.core.tasks.analysis.diffex

Methods in ubic.gemma.core.tasks.analysis.diffex that return ExperimentalFactor

Modifier and Type	Method	Description
ExperimentalFactor	DifferentialExpressionAnalysisTaskCommand.getSubsetFactor()

Methods in ubic.gemma.core.tasks.analysis.diffex that return types with arguments of type ExperimentalFactor

Modifier and Type	Method	Description
Collection<ExperimentalFactor>	DifferentialExpressionAnalysisTaskCommand.getFactors()

Methods in ubic.gemma.core.tasks.analysis.diffex with parameters of type ExperimentalFactor

Modifier and Type	Method	Description
void	DifferentialExpressionAnalysisTaskCommand.setSubsetFactor(ExperimentalFactor subsetFactor)

Method parameters in ubic.gemma.core.tasks.analysis.diffex with type arguments of type ExperimentalFactor

Modifier and Type	Method	Description
void	DifferentialExpressionAnalysisTaskCommand.setFactors(Collection<ExperimentalFactor> factors)

Uses of ExperimentalFactor in ubic.gemma.core.visualization

Methods in ubic.gemma.core.visualization that return types with arguments of type ExperimentalFactor

Modifier and Type	Method	Description
Map<Long,LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>>>	ExperimentalDesignVisualizationService.sortVectorDataByDesign(Collection<DoubleVectorValueObject> dedVs)	Put data vectors in the order you'd want to display the experimental design.
Map<Long,LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>>>	ExperimentalDesignVisualizationService.sortVectorDataByDesign(Collection<DoubleVectorValueObject> dedVs, ExperimentalFactor primaryFactor)	Put data vectors in the order you'd want to display the experimental design.
Map<Long,LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>>>	ExperimentalDesignVisualizationServiceImpl.sortVectorDataByDesign(Collection<DoubleVectorValueObject> dedVs)
Map<Long,LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>>>	ExperimentalDesignVisualizationServiceImpl.sortVectorDataByDesign(Collection<DoubleVectorValueObject> dedVs, ExperimentalFactor primaryFactor)

Methods in ubic.gemma.core.visualization with parameters of type ExperimentalFactor

Modifier and Type	Method	Description
Map<Long,LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>>>	ExperimentalDesignVisualizationService.sortVectorDataByDesign(Collection<DoubleVectorValueObject> dedVs, ExperimentalFactor primaryFactor)	Put data vectors in the order you'd want to display the experimental design.
Map<Long,LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>>>	ExperimentalDesignVisualizationServiceImpl.sortVectorDataByDesign(Collection<DoubleVectorValueObject> dedVs, ExperimentalFactor primaryFactor)

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

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

Modifier and Type	Method	Description
Set<ExperimentalFactor>	FactorAssociatedAnalysisResultSet.getExperimentalFactors()

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

Modifier and Type	Method	Description
void	FactorAssociatedAnalysisResultSet.setExperimentalFactors(Set<ExperimentalFactor> experimentalFactors)

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

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

Modifier and Type	Method	Description
static ExpressionAnalysisResultSet	ExpressionAnalysisResultSet.Factory.newInstance(Set<ExperimentalFactor> experimentalFactors, Integer numberOfProbesTested, Integer numberOfGenesTested, FactorValue baselineGroup, Set<DifferentialExpressionAnalysisResult> results, DifferentialExpressionAnalysis analysis, PvalueDistribution pvalueDistribution, Set<HitListSize> hitListSizes)

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

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

Modifier and Type	Method	Description
ExperimentalFactor	FactorValue.getExperimentalFactor()
static ExperimentalFactor	ExperimentalFactor.Factory.newInstance()

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

Modifier and Type	Method	Description
Set<ExperimentalFactor>	ExperimentalDesign.getExperimentalFactors()

Methods in ubic.gemma.model.expression.experiment with parameters of type ExperimentalFactor

Modifier and Type	Method	Description
static FactorValue	FactorValue.Factory.newInstance(ExperimentalFactor experimentalFactor)
void	FactorValue.setExperimentalFactor(ExperimentalFactor experimentalFactor)

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

Modifier and Type	Method	Description
void	ExperimentalDesign.setExperimentalFactors(Set<ExperimentalFactor> experimentalFactors)

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

Constructor	Description
ExperimentalFactorValueObject(ExperimentalFactor factor)

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

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

Modifier and Type	Method	Description
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisDao.findByFactor(ExperimentalFactor ef)	Retrieve analyses associated with the factor, either through the subset factor or as factors for result sets.
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisService.findByFactor(ExperimentalFactor ef)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisServiceImpl.findByFactor(ExperimentalFactor ef)
int	DifferentialExpressionAnalysisService.removeForExperimentalFactor(ExperimentalFactor experimentalFactor)	Remove analyses using the given factor.
int	DifferentialExpressionAnalysisServiceImpl.removeForExperimentalFactor(ExperimentalFactor experimentalFactor)

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

Modifier and Type	Method	Description
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisDao.findByFactors(Collection<ExperimentalFactor> experimentalFactors)
int	DifferentialExpressionAnalysisService.removeForExperimentalFactors(Collection<ExperimentalFactor> experimentalFactors)
int	DifferentialExpressionAnalysisServiceImpl.removeForExperimentalFactors(Collection<ExperimentalFactor> experimentalFactors)

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

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

Modifier and Type	Method	Description
ExperimentalFactor	ExpressionExperimentService.addFactor(ExpressionExperiment ee, ExperimentalFactor factor)
ExperimentalFactor	ExpressionExperimentServiceImpl.addFactor(ExpressionExperiment ee, ExperimentalFactor factor)
ExperimentalFactor	ExperimentalFactorDao.find(ExperimentalFactor experimentalFactor)
ExperimentalFactor	ExperimentalFactorDaoImpl.find(ExperimentalFactor experimentalFactor)
ExperimentalFactor	ExperimentalFactorService.find(ExperimentalFactor experimentalFactor)
ExperimentalFactor	ExperimentalFactorDao.findOrCreate(ExperimentalFactor experimentalFactor)
ExperimentalFactor	ExperimentalFactorService.findOrCreate(ExperimentalFactor experimentalFactor)
ExperimentalFactor	ExperimentalFactorDaoImpl.load(Long id)
ExperimentalFactor	ExperimentalFactorService.load(Long id)
ExperimentalFactor	ExperimentalFactorDao.thaw(ExperimentalFactor ef)
ExperimentalFactor	ExperimentalFactorDaoImpl.thaw(ExperimentalFactor ef)
ExperimentalFactor	ExperimentalFactorService.thaw(ExperimentalFactor ef)
ExperimentalFactor	ExperimentalFactorServiceImpl.thaw(ExperimentalFactor ef)

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

Modifier and Type	Method	Description
Collection<ExperimentalFactor>	ExperimentalFactorService.load(Collection<Long> ids)
Collection<ExperimentalFactor>	ExperimentalFactorService.loadAll()

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

Modifier and Type	Method	Description
ExperimentalFactor	ExpressionExperimentService.addFactor(ExpressionExperiment ee, ExperimentalFactor factor)
ExperimentalFactor	ExpressionExperimentServiceImpl.addFactor(ExpressionExperiment ee, ExperimentalFactor factor)
protected ExperimentalFactorValueObject	ExperimentalFactorDaoImpl.doLoadValueObject(ExperimentalFactor e)
ExperimentalFactor	ExperimentalFactorDao.find(ExperimentalFactor experimentalFactor)
ExperimentalFactor	ExperimentalFactorDaoImpl.find(ExperimentalFactor experimentalFactor)
ExperimentalFactor	ExperimentalFactorService.find(ExperimentalFactor experimentalFactor)
ExpressionExperiment	ExpressionExperimentDao.findByFactor(ExperimentalFactor ef)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByFactor(ExperimentalFactor ef)
ExpressionExperiment	ExpressionExperimentService.findByFactor(ExperimentalFactor factor)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByFactor(ExperimentalFactor factor)
ExperimentalFactor	ExperimentalFactorDao.findOrCreate(ExperimentalFactor experimentalFactor)
ExperimentalFactor	ExperimentalFactorService.findOrCreate(ExperimentalFactor experimentalFactor)
Collection<FactorValue>	ExpressionExperimentSubSetDao.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)
Collection<FactorValue>	ExpressionExperimentSubSetDaoImpl.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)
Collection<FactorValue>	ExpressionExperimentSubSetService.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)
Collection<FactorValue>	ExpressionExperimentSubSetServiceImpl.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)
void	ExperimentalFactorDaoImpl.remove(ExperimentalFactor experimentalFactor)
void	ExperimentalFactorService.remove(ExperimentalFactor experimentalFactor)	Delete the factor, its associated factor values and all differential expression analyses in which it is used.
void	ExperimentalFactorServiceImpl.remove(ExperimentalFactor experimentalFactor)
ExperimentalFactor	ExperimentalFactorDao.thaw(ExperimentalFactor ef)
ExperimentalFactor	ExperimentalFactorDaoImpl.thaw(ExperimentalFactor ef)
ExperimentalFactor	ExperimentalFactorService.thaw(ExperimentalFactor ef)
ExperimentalFactor	ExperimentalFactorServiceImpl.thaw(ExperimentalFactor ef)
void	ExperimentalFactorService.update(ExperimentalFactor experimentalFactor)

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

Modifier and Type	Method	Description
void	ExperimentalFactorService.remove(Collection<ExperimentalFactor> entities)
void	ExperimentalFactorServiceImpl.remove(Collection<ExperimentalFactor> experimentalFactors)
void	ExperimentalFactorService.update(Collection<ExperimentalFactor> entities)

Uses of ExperimentalFactor in ubic.gemma.persistence.util

Methods in ubic.gemma.persistence.util that return types with arguments of type ExperimentalFactor

Modifier and Type	Method	Description
List<ExperimentalFactor>	FactorValueVector.getFactors()

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

Modifier and Type	Method	Description
static void	BusinessKey.addRestrictions(Criteria queryObject, ExperimentalFactor experimentalFactor)
static void	BusinessKey.checkValidKey(ExperimentalFactor experimentalFactor)
Collection<FactorValue>	FactorValueVector.getValuesForFactor(ExperimentalFactor factor)

Constructor parameters in ubic.gemma.persistence.util with type arguments of type ExperimentalFactor

Constructor	Description
FactorValueVector(Collection<ExperimentalFactor> factors, Collection<FactorValue> values)

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

Method parameters in ubic.gemma.web.controller.expression.experiment with type arguments of type ExperimentalFactor

Modifier and Type	Method	Description
void	ExperimentalDesignController.createFactorValue(EntityDelegator<ExperimentalFactor> e)
void	ExperimentalDesignController.deleteFactorValues(EntityDelegator<ExperimentalFactor> e, Long[] fvIds)
Collection<FactorValueValueObject>	ExperimentalDesignController.getFactorValues(EntityDelegator<ExperimentalFactor> e)
Collection<FactorValueValueObject>	ExpressionExperimentController.getFactorValues(EntityDelegator<ExperimentalFactor> e)	AJAX
Collection<FactorValueValueObject>	ExperimentalDesignController.getFactorValuesWithCharacteristics(EntityDelegator<ExperimentalFactor> e)

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

Method parameters in ubic.gemma.web.controller.visualization with type arguments of type ExperimentalFactor

Modifier and Type	Method	Description
void	VisualizationValueObject.setUpFactorProfiles(LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>> layout)	Initialize the factor profiles.

Constructors in ubic.gemma.web.controller.visualization with parameters of type ExperimentalFactor

Constructor	Description
FactorProfile(ExperimentalFactor ef, LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>> layouts)

Constructor parameters in ubic.gemma.web.controller.visualization with type arguments of type ExperimentalFactor

Constructor	Description
FactorProfile(ExperimentalFactor ef, LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>> layouts)