Package ubic.gemma.persistence.service.expression.bioAssayData

Interface ProcessedExpressionDataVectorDao

All Superinterfaces:

BaseDao<ProcessedExpressionDataVector>, DesignElementDataVectorDao<ProcessedExpressionDataVector>

All Known Implementing Classes:

ProcessedExpressionDataVectorDaoImpl

public interface ProcessedExpressionDataVectorDao
extends DesignElementDataVectorDao<ProcessedExpressionDataVector>

Author:

Paul

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	ProcessedExpressionDataVectorDao.RankMethod

Method Summary

Modifier and Type	Method	Description
void	clearCache()
Set<ProcessedExpressionDataVector>	createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean ignoreQuantitationMismatch)	Populate the processed data for the given experiment.
Collection<ProcessedExpressionDataVector>	find(Collection<CompositeSequence> designElements, QuantitationType quantitationType)
Collection<ProcessedExpressionDataVector>	find(ArrayDesign arrayDesign, QuantitationType quantitationType)
Collection<ProcessedExpressionDataVector>	findByExpressionExperiment(ExpressionExperiment ee, QuantitationType quantitationType)
Collection<DoubleVectorValueObject>	getProcessedDataArrays(Collection<? extends BioAssaySet> expressionExperiments, Collection<Long> genes)
Collection<DoubleVectorValueObject>	getProcessedDataArrays(BioAssaySet expressionExperiment)
Collection<DoubleVectorValueObject>	getProcessedDataArrays(BioAssaySet expressionExperiment, int limit)
Collection<DoubleVectorValueObject>	getProcessedDataArrays(BioAssaySet expressionExperiment, Collection<Long> genes)
Collection<DoubleVectorValueObject>	getProcessedDataArraysByProbe(Collection<? extends BioAssaySet> expressionExperiments, Collection<CompositeSequence> probes)
Collection<DoubleVectorValueObject>	getProcessedDataArraysByProbeIds(BioAssaySet ee, Collection<Long> probes)
Collection<ProcessedExpressionDataVector>	getProcessedVectors(ExpressionExperiment expressionExperiment)
Map<ExpressionExperiment,Map<Gene,Collection<Double>>>	getRanks(Collection<ExpressionExperiment> expressionExperiments, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<Gene,Collection<Double>>	getRanks(ExpressionExperiment expressionExperiment, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<CompositeSequence,Double>	getRanks(ExpressionExperiment expressionExperiment, ProcessedExpressionDataVectorDao.RankMethod method)
Map<ExpressionExperiment,Map<Gene,Map<CompositeSequence,Double[]>>>	getRanksByProbe(Collection<ExpressionExperiment> expressionExperiments, Collection<Gene> genes)	Retrieve expression level information for genes in experiments.
void	removeProcessedDataVectors(ExpressionExperiment expressionExperiment)

Methods inherited from interface ubic.gemma.persistence.service.BaseDao

countAll, create, create, find, findOrCreate, getElementClass, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, remove, remove, remove, save, save, update, update

Methods inherited from interface ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDao

find, find, find, findByExpressionExperiment, thaw, thaw

Method Detail

clearCache

void clearCache()

createProcessedDataVectors

Set<ProcessedExpressionDataVector> createProcessedDataVectors(ExpressionExperiment expressionExperiment,
                                                              boolean ignoreQuantitationMismatch)
                                                       throws QuantitationMismatchException

Populate the processed data for the given experiment. For two-channel studies, the missing value information should already have been computed. If the values already exist, they will be re-written. The data will be quantile normalized (with some exceptions: ratios and count data will not be normalized).

Parameters:

expressionExperiment - ee

ignoreQuantitationMismatch - use raw data to infer scale type and the adequate transformation for producing processed EVs instead of relying on the QT

Returns:

the created processed vectors

Throws:

QuantitationMismatchException

getProcessedDataArrays

Collection<DoubleVectorValueObject> getProcessedDataArrays(BioAssaySet expressionExperiment)

getProcessedDataArrays

Collection<DoubleVectorValueObject> getProcessedDataArrays(BioAssaySet expressionExperiment,
                                                           Collection<Long> genes)

getProcessedDataArrays

Collection<DoubleVectorValueObject> getProcessedDataArrays(BioAssaySet expressionExperiment,
                                                           int limit)

getProcessedDataArrays

Collection<DoubleVectorValueObject> getProcessedDataArrays(Collection<? extends BioAssaySet> expressionExperiments,
                                                           Collection<Long> genes)

getProcessedDataArraysByProbe

Collection<DoubleVectorValueObject> getProcessedDataArraysByProbe(Collection<? extends BioAssaySet> expressionExperiments,
                                                                  Collection<CompositeSequence> probes)

getProcessedDataArraysByProbeIds

Collection<DoubleVectorValueObject> getProcessedDataArraysByProbeIds(BioAssaySet ee,
                                                                     Collection<Long> probes)

getProcessedVectors

Collection<ProcessedExpressionDataVector> getProcessedVectors(ExpressionExperiment expressionExperiment)

Parameters:

expressionExperiment - ee

Returns:

Processed data for the given experiment. NOTE the vectors are thawed before returning.

getRanks

Map<ExpressionExperiment,Map<Gene,Collection<Double>>> getRanks(Collection<ExpressionExperiment> expressionExperiments,
                                                                            Collection<Gene> genes,
                                                                            ProcessedExpressionDataVectorDao.RankMethod method)

getRanks

Map<Gene,Collection<Double>> getRanks(ExpressionExperiment expressionExperiment,
                                            Collection<Gene> genes,
                                            ProcessedExpressionDataVectorDao.RankMethod method)

getRanks

Map<CompositeSequence,Double> getRanks(ExpressionExperiment expressionExperiment,
                                             ProcessedExpressionDataVectorDao.RankMethod method)

getRanksByProbe

Map<ExpressionExperiment,Map<Gene,Map<CompositeSequence,Double[]>>> getRanksByProbe(Collection<ExpressionExperiment> expressionExperiments,
                                                                                                      Collection<Gene> genes)

Retrieve expression level information for genes in experiments.

Parameters:

genes - genes

expressionExperiments - expression experiments

Returns:

A map of experiment -> gene -> probe -> array of doubles holding the 1) mean and 2) max expression rank.

removeProcessedDataVectors

void removeProcessedDataVectors(ExpressionExperiment expressionExperiment)

find

Collection<ProcessedExpressionDataVector> find(ArrayDesign arrayDesign,
                                               QuantitationType quantitationType)

find

Collection<ProcessedExpressionDataVector> find(Collection<CompositeSequence> designElements,
                                               QuantitationType quantitationType)

findByExpressionExperiment

Collection<ProcessedExpressionDataVector> findByExpressionExperiment(ExpressionExperiment ee,
                                                                     QuantitationType quantitationType)