Uses of Class
ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult

Packages that use DifferentialExpressionAnalysisResult

Package	Description
ubic.gemma.core.analysis.service
ubic.gemma.model.analysis.expression.diff
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.util
ubic.gemma.rest

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

Method parameters in ubic.gemma.core.analysis.service with type arguments of type DifferentialExpressionAnalysisResult

Modifier and Type	Method	Description
void	DifferentialExpressionAnalysisResultListFileService.writeTsv(List<DifferentialExpressionAnalysisResult> payload, Gene gene, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, Writer writer)	Writes a list of DE results with additional columns for mapping them to source experiments and analyzed experiments (for subsets).
void	DifferentialExpressionAnalysisResultListFileService.writeTsv(List<DifferentialExpressionAnalysisResult> payload, Gene gene, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, Writer writer)	Writes a list of DE results with additional columns for mapping them to source experiments and analyzed experiments (for subsets).
void	DifferentialExpressionAnalysisResultListFileServiceImpl.writeTsv(List<DifferentialExpressionAnalysisResult> entity, Gene gene, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, Writer writer)
void	DifferentialExpressionAnalysisResultListFileServiceImpl.writeTsv(List<DifferentialExpressionAnalysisResult> entity, Gene gene, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, Writer writer)

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

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

Modifier and Type	Method	Description
static DifferentialExpressionAnalysisResult	DifferentialExpressionAnalysisResult.Factory.newInstance()

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

Modifier and Type	Method	Description
Set<DifferentialExpressionAnalysisResult>	ExpressionAnalysisResultSet.getResults()
Set<DifferentialExpressionAnalysisResult>	GeneDifferentialExpressionMetaAnalysisResult.getResultsUsed()

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

Modifier and Type	Method	Description
void	ExpressionAnalysisResultSet.setResults(Set<DifferentialExpressionAnalysisResult> results)
void	GeneDifferentialExpressionMetaAnalysisResult.setResultsUsed(Set<DifferentialExpressionAnalysisResult> resultsUsed)

Constructors in ubic.gemma.model.analysis.expression.diff with parameters of type DifferentialExpressionAnalysisResult

Modifier	Constructor	Description
	ContrastsValueObject(DifferentialExpressionAnalysisResult o)
	DifferentialExpressionAnalysisResultValueObject(DifferentialExpressionAnalysisResult result, boolean includeFactorValues)
	DifferentialExpressionAnalysisResultValueObject(DifferentialExpressionAnalysisResult result, boolean includeFactorValuesInContrasts, Set<Gene> genes, boolean includeTaxonInGenes)
	DifferentialExpressionValueObject(DifferentialExpressionAnalysisResult o)

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

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

Modifier and Type	Method	Description
Collection<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultDaoImpl.create(Collection<DifferentialExpressionAnalysisResult> entities)
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,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)
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultDao.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentAnalyzedIds, boolean includeSubsets, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, double threshold, boolean keepNonSpecificProbes, boolean initializeFactorValues)	Retrieve differential expression results for a given gene across all the given datasets.
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)
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultDaoImpl.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentAnalyzedIds, boolean includeSubsets, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, double threshold, boolean keepNonSpecificProbes, boolean initializeFactorValues)
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultService.findByGeneAndExperimentAnalyzedIds(Gene gene, boolean keepNonSpecific, Collection<Long> experimentAnalyzedIds, boolean includeSubSets, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, double threshold, boolean initializeFactorValues)
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultServiceImpl.findByGeneAndExperimentAnalyzedIds(Gene gene, boolean keepNonSpecific, Collection<Long> experimentAnalyzedIds, boolean includeSubSets, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, double threshold, boolean initializeFactorValues)
Collection<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultDaoImpl.loadAll()

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

Modifier and Type	Method	Description
void	DifferentialExpressionResultDaoImpl.remove(DifferentialExpressionAnalysisResult entity)

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

Modifier and Type	Method	Description
Collection<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultDaoImpl.create(Collection<DifferentialExpressionAnalysisResult> entities)
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultDao.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentAnalyzedIds, boolean includeSubsets, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, double threshold, boolean keepNonSpecificProbes, boolean initializeFactorValues)	Retrieve differential expression results for a given gene across all the given datasets.
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultDaoImpl.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentAnalyzedIds, boolean includeSubsets, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, double threshold, boolean keepNonSpecificProbes, boolean initializeFactorValues)
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultService.findByGeneAndExperimentAnalyzedIds(Gene gene, boolean keepNonSpecific, Collection<Long> experimentAnalyzedIds, boolean includeSubSets, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, double threshold, boolean initializeFactorValues)
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultServiceImpl.findByGeneAndExperimentAnalyzedIds(Gene gene, boolean keepNonSpecific, Collection<Long> experimentAnalyzedIds, boolean includeSubSets, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, double threshold, boolean initializeFactorValues)

Uses of DifferentialExpressionAnalysisResult in ubic.gemma.persistence.util

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

Modifier and Type	Method	Description
int	DifferentialExpressionAnalysisResultComparator.compare(DifferentialExpressionAnalysisResult ear1, DifferentialExpressionAnalysisResult ear2)

Uses of DifferentialExpressionAnalysisResult in ubic.gemma.rest

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

Modifier	Constructor	Description
	DifferentialExpressionAnalysisResultByGeneValueObject(DifferentialExpressionAnalysisResult result, Long sourceExperimentId, Long experimentAnalyzedId, Baseline baseline)