Uses of Class
ubic.gemma.model.expression.experiment.ExpressionExperiment
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Uses of ExpressionExperiment in ubic.gemma.core.analysis.expression
Methods in ubic.gemma.core.analysis.expression with parameters of type ExpressionExperiment Modifier and Type Method Description boolean
AnalysisUtilService. deleteOldAnalyses(ExpressionExperiment expExp)
Remove all analyses for the experiment (Differential, Coexpression and PCA).boolean
AnalysisUtilServiceImpl. deleteOldAnalyses(ExpressionExperiment expExp)
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Uses of ExpressionExperiment in ubic.gemma.core.analysis.expression.coexpression.links
Methods in ubic.gemma.core.analysis.expression.coexpression.links with parameters of type ExpressionExperiment Modifier and Type Method Description LinkAnalysis
LinkAnalysisService. process(ExpressionExperiment ee, FilterConfig filterConfig, LinkAnalysisConfig linkAnalysisConfig)
Run a link analysis on an experiment, and persist the results if the configuration says to.LinkAnalysis
LinkAnalysisServiceImpl. process(ExpressionExperiment ee, FilterConfig filterConfig, LinkAnalysisConfig linkAnalysisConfig)
Constructors in ubic.gemma.core.analysis.expression.coexpression.links with parameters of type ExpressionExperiment Constructor Description UnsuitableForAnalysisException(ExpressionExperiment ee, String string)
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Uses of ExpressionExperiment in ubic.gemma.core.analysis.expression.diff
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Uses of ExpressionExperiment in ubic.gemma.core.analysis.preprocess
Methods in ubic.gemma.core.analysis.preprocess that return ExpressionExperiment Modifier and Type Method Description ExpressionExperiment
ExpressionDataMatrixBuilder. getExpressionExperiment()
Methods in ubic.gemma.core.analysis.preprocess with parameters of type ExpressionExperiment Modifier and Type Method Description Collection<RawExpressionDataVector>
TwoChannelMissingValues. computeMissingValues(ExpressionExperiment ee)
Collection<RawExpressionDataVector>
TwoChannelMissingValues. computeMissingValues(ExpressionExperiment ee, double signalToNoiseThreshold, Collection<Double> extraMissingValueIndicators)
Collection<RawExpressionDataVector>
TwoChannelMissingValuesImpl. computeMissingValues(ExpressionExperiment ee)
Collection<RawExpressionDataVector>
TwoChannelMissingValuesImpl. computeMissingValues(ExpressionExperiment ee, double signalToNoiseThreshold, Collection<Double> extraMissingValueIndicators)
MeanVarianceRelation
MeanVarianceService. create(ExpressionExperiment ee, boolean forceRecompute)
Retrieve (and if necessary compute) the mean-variance relationship for the experimentMeanVarianceRelation
MeanVarianceServiceImpl. create(ExpressionExperiment ee, boolean forceRecompute)
void
MeanVarianceServiceHelper. createMeanVariance(ExpressionExperiment ee, MeanVarianceRelation mvr)
ExpressionDataDoubleMatrix
MeanVarianceServiceHelper. getIntensities(ExpressionExperiment ee)
static Collection<QuantitationType>
ExpressionDataMatrixBuilder. getMissingValueQuantitationTypes(ExpressionExperiment expressionExperiment)
Collection<OutlierDetails>
OutlierDetectionService. getOutlierDetails(ExpressionExperiment ee)
Obtain existing outlier details from a previousOutlierDetectionService.identifyOutliersByMedianCorrelation(ExpressionExperiment)
invocation.Collection<OutlierDetails>
OutlierDetectionServiceImpl. getOutlierDetails(ExpressionExperiment ee)
static Collection<QuantitationType>
ExpressionDataMatrixBuilder. getPreferredAndMissingQuantitationTypes(ExpressionExperiment expressionExperiment)
static Collection<QuantitationType>
ExpressionDataMatrixBuilder. getPreferredQuantitationTypes(ExpressionExperiment expressionExperiment)
static Collection<QuantitationType>
ExpressionDataMatrixBuilder. getUsefulQuantitationTypes(ExpressionExperiment expressionExperiment)
Collection<OutlierDetails>
OutlierDetectionService. identifyOutliersByMedianCorrelation(ExpressionExperiment ee)
Identify outliers by median correlation for the given dataset.Collection<OutlierDetails>
OutlierDetectionServiceImpl. identifyOutliersByMedianCorrelation(ExpressionExperiment ee)
void
VectorMergingService. mergeVectors(ExpressionExperiment expExp)
void
VectorMergingServiceImpl. mergeVectors(ExpressionExperiment ee)
Collection<RawExpressionDataVector>
TwoChannelMissingValueHelperService. persist(ExpressionExperiment source, Collection<RawExpressionDataVector> results)
default void
PreprocessorService. process(ExpressionExperiment ee)
Preprocess a dataset.default void
PreprocessorService. process(ExpressionExperiment ee, boolean ignoreQuantitationMismatch)
Preprocess a dataset.void
PreprocessorService. process(ExpressionExperiment ee, boolean ignoreQuantitationMismatch, boolean ignoreDiagnosticFailure)
Preprocess a dataset.void
PreprocessorServiceImpl. process(ExpressionExperiment ee, boolean ignoreQuantitationMismatch, boolean ignoreDiagnosticsFailure)
void
PreprocessorService. processDiagnostics(ExpressionExperiment ee)
Create or update the sample correlation, PCA and M-V data.void
PreprocessorServiceImpl. processDiagnostics(ExpressionExperiment ee)
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)
Constructors in ubic.gemma.core.analysis.preprocess with parameters of type ExpressionExperiment Constructor Description FailedToComputeSingularValueDecomposition(ExpressionExperiment ee, SVDException cause)
InsufficientProbesException(ExpressionExperiment ee, String message)
PreprocessingException(ExpressionExperiment ee, String message)
PreprocessingException(ExpressionExperiment ee, Throwable cause)
QuantitationMismatchPreprocessingException(ExpressionExperiment ee, QuantitationMismatchException cause)
SampleCoexpressionRelatedPreprocessingException(ExpressionExperiment ee, Throwable cause)
SVDRelatedPreprocessingException(ExpressionExperiment ee, SVDException cause)
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Uses of ExpressionExperiment in ubic.gemma.core.analysis.preprocess.batcheffects
Methods in ubic.gemma.core.analysis.preprocess.batcheffects with parameters of type ExpressionExperiment Modifier and Type Method Description boolean
ExpressionExperimentBatchCorrectionService. checkCorrectability(ExpressionExperiment ee)
Is there a Batch factor provided? Is there a confound problem? Do we have at least two samples per batch? This will return true even if there is evidence the data has been batch-corrected before; we assume the caller wants to redo it based on the raw databoolean
ExpressionExperimentBatchCorrectionServiceImpl. checkCorrectability(ExpressionExperiment ee)
ExpressionDataDoubleMatrix
ExpressionExperimentBatchCorrectionService. comBat(ExpressionExperiment ee)
ExpressionDataDoubleMatrix
ExpressionExperimentBatchCorrectionServiceImpl. comBat(ExpressionExperiment ee)
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 informationExperimentalFactor
BatchInfoPopulationHelperServiceImpl. createRnaSeqBatchFactor(ExpressionExperiment ee, Map<BioMaterial,String> headers)
void
BatchInfoPopulationService. fillBatchInformation(ExpressionExperiment ee, boolean force)
Attempt to obtain batch information from the data provider and populate it into the given experiment.void
BatchInfoPopulationServiceImpl. fillBatchInformation(ExpressionExperiment ee, boolean force)
static Map<String,BioAssay>
BatchInfoParser. getAccessionToBioAssayMap(ExpressionExperiment ee)
ExperimentalFactor
ExpressionExperimentBatchCorrectionService. getBatchFactor(ExpressionExperiment ee)
For convenience of some testing classesExperimentalFactor
ExpressionExperimentBatchCorrectionServiceImpl. getBatchFactor(ExpressionExperiment ee)
Map<BioMaterial,Date>
BatchInfoParser. getBatchInfo(ExpressionExperiment ee, Collection<LocalFile> files)
static ExpressionDataDoubleMatrix
ExpressionExperimentBatchCorrectionServiceImpl. removeOutliers(ExpressionDataDoubleMatrix originalDataMatrix, ExpressionExperiment ee)
Remove outlier samples from the data matrix, based on outliers that were flagged in the experiment (not just candidate outliers)Constructors in ubic.gemma.core.analysis.preprocess.batcheffects with parameters of type ExpressionExperiment Constructor Description BatchInfoPopulationException(ExpressionExperiment ee, String message)
BatchInfoPopulationException(ExpressionExperiment ee, Throwable cause)
FASTQHeadersPresentButNotUsableException(ExpressionExperiment ee, String message)
SingletonBatchesException(ExpressionExperiment ee, String message)
UnsupportedRawdataFileFormatException(ExpressionExperiment ee, String message)
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Uses of ExpressionExperiment in ubic.gemma.core.analysis.preprocess.filter
Constructors in ubic.gemma.core.analysis.preprocess.filter with parameters of type ExpressionExperiment Constructor Description FilteringException(ExpressionExperiment ee, String message)
InsufficientDataException(ExpressionExperiment ee, String message)
InsufficientSamplesException(ExpressionExperiment ee, String message)
NoRowsLeftAfterFilteringException(ExpressionExperiment ee, String message)
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Uses of ExpressionExperiment in ubic.gemma.core.analysis.preprocess.svd
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Uses of ExpressionExperiment in ubic.gemma.core.analysis.report
Methods in ubic.gemma.core.analysis.report that return types with arguments of type ExpressionExperiment Modifier and Type Method Description Collection<ExpressionExperiment>
WhatsNew. getNewExpressionExperiments()
Collection<ExpressionExperiment>
WhatsNew. getUpdatedExpressionExperiments()
Methods in ubic.gemma.core.analysis.report with parameters of type ExpressionExperiment Modifier and Type Method Description void
ExpressionExperimentReportService. recalculateExperimentBatchInfo(ExpressionExperiment ee)
Recalculates the batch effect and batch confound information for the given dataset.void
ExpressionExperimentReportServiceImpl. recalculateExperimentBatchInfo(ExpressionExperiment ee)
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Uses of ExpressionExperiment in ubic.gemma.core.analysis.service
Methods in ubic.gemma.core.analysis.service that return types with arguments of type ExpressionExperiment Modifier and Type Method Description DoubleMatrix<Gene,ExpressionExperiment>
ExpressionDataMatrixService. getRankMatrix(Collection<Gene> genes, Collection<ExpressionExperiment> ees, ProcessedExpressionDataVectorDao.RankMethod method)
DoubleMatrix<Gene,ExpressionExperiment>
ExpressionDataMatrixServiceImpl. getRankMatrix(Collection<Gene> genes, Collection<ExpressionExperiment> ees, ProcessedExpressionDataVectorDao.RankMethod method)
Methods in ubic.gemma.core.analysis.service with parameters of type ExpressionExperiment Modifier and Type Method Description void
ExpressionDataFileService. deleteAllFiles(ExpressionExperiment ee)
Delete any existing coexpression, data, or differential expression data files.void
ExpressionDataFileServiceImpl. deleteAllFiles(ExpressionExperiment ee)
ExpressionDataDoubleMatrix
ExpressionDataMatrixService. getFilteredMatrix(ExpressionExperiment ee, FilterConfig filterConfig)
Provide a filtered expression data matrix.ExpressionDataDoubleMatrix
ExpressionDataMatrixService. getFilteredMatrix(ExpressionExperiment ee, FilterConfig filterConfig, Collection<ProcessedExpressionDataVector> dataVectors)
Provide a filtered expression data matrix.ExpressionDataDoubleMatrix
ExpressionDataMatrixServiceImpl. getFilteredMatrix(ExpressionExperiment ee, FilterConfig filterConfig)
ExpressionDataDoubleMatrix
ExpressionDataMatrixServiceImpl. getFilteredMatrix(ExpressionExperiment ee, FilterConfig filterConfig, Collection<ProcessedExpressionDataVector> dataVectors)
File
ExpressionDataFileService. getMetadataFile(ExpressionExperiment ee, ExpressionExperimentMetaFileType type)
Locate a metadata file.File
ExpressionDataFileServiceImpl. getMetadataFile(ExpressionExperiment ee, ExpressionExperimentMetaFileType type)
File
ExpressionDataFileService. getOutputFile(ExpressionExperiment ee, boolean filtered)
File
ExpressionDataFileService. getOutputFile(ExpressionExperiment ee, boolean filtered, boolean compressed, boolean temporary)
File
ExpressionDataFileServiceImpl. getOutputFile(ExpressionExperiment ee, boolean filtered)
File
ExpressionDataFileServiceImpl. getOutputFile(ExpressionExperiment ee, boolean filtered, boolean compressed, boolean temporary)
ExpressionDataDoubleMatrix
ExpressionDataMatrixService. getProcessedExpressionDataMatrix(ExpressionExperiment ee)
ExpressionDataDoubleMatrix
ExpressionDataMatrixServiceImpl. getProcessedExpressionDataMatrix(ExpressionExperiment ee)
ExpressionDataDoubleMatrix
ExpressionDataMatrixService. getRawExpressionDataMatrix(ExpressionExperiment ee, QuantitationType quantitationType)
Obtain a raw expression data matrix for a given quantitation typeExpressionDataDoubleMatrix
ExpressionDataMatrixServiceImpl. getRawExpressionDataMatrix(ExpressionExperiment ee, QuantitationType quantitationType)
Optional<File>
ExpressionDataFileService. writeOrLocateCoexpressionDataFile(ExpressionExperiment ee, boolean forceWrite)
Write or located the coexpression data file for a given experimentOptional<File>
ExpressionDataFileServiceImpl. writeOrLocateCoexpressionDataFile(ExpressionExperiment ee, boolean forceWrite)
File
ExpressionDataFileService. writeOrLocateDesignFile(ExpressionExperiment ee, boolean forceWrite)
Locate or create an experimental design file for a given experiment.File
ExpressionDataFileServiceImpl. writeOrLocateDesignFile(ExpressionExperiment ee, boolean forceWrite)
Collection<File>
ExpressionDataFileService. writeOrLocateDiffExpressionDataFiles(ExpressionExperiment ee, boolean forceWrite)
Locate or create the differential expression data file(s) for a given experiment.Collection<File>
ExpressionDataFileServiceImpl. writeOrLocateDiffExpressionDataFiles(ExpressionExperiment ee, boolean forceWrite)
Optional<File>
ExpressionDataFileService. writeOrLocateJSONProcessedExpressionDataFile(ExpressionExperiment ee, boolean forceWrite, boolean filtered)
Optional<File>
ExpressionDataFileServiceImpl. writeOrLocateJSONProcessedExpressionDataFile(ExpressionExperiment ee, boolean forceWrite, boolean filtered)
File
ExpressionDataFileService. writeOrLocateJSONRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite)
File
ExpressionDataFileServiceImpl. writeOrLocateJSONRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite)
Optional<File>
ExpressionDataFileService. writeOrLocateProcessedDataFile(ExpressionExperiment ee, boolean forceWrite, boolean filtered)
Locate or create a data file containing the 'preferred and masked' expression data matrix, with filtering for low expression applied (currently supports default settings only).Optional<File>
ExpressionDataFileServiceImpl. writeOrLocateProcessedDataFile(ExpressionExperiment ee, boolean forceWrite, boolean filtered)
File
ExpressionDataFileService. writeOrLocateRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite)
Locate or create a new data file for the given quantitation type.File
ExpressionDataFileServiceImpl. writeOrLocateRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite)
void
ExpressionDataFileService. writeProcessedExpressionData(ExpressionExperiment ee, Writer writer)
Write processed expression data to a given writer for a given quantitation type.void
ExpressionDataFileServiceImpl. writeProcessedExpressionData(ExpressionExperiment ee, Writer writer)
Optional<File>
ExpressionDataFileService. writeProcessedExpressionDataFile(ExpressionExperiment ee, boolean filtered, String fileName, boolean compress)
Create a data file containing the 'preferred and masked' expression data matrix, with filtering for low expression applied (currently supports default settings only).Optional<File>
ExpressionDataFileServiceImpl. writeProcessedExpressionDataFile(ExpressionExperiment ee, boolean filtered, String fileName, boolean compress)
void
ExpressionDataFileService. writeRawExpressionData(ExpressionExperiment ee, QuantitationType qt, Writer writer)
Write raw expression data to a given writer for a given quantitation type.void
ExpressionDataFileServiceImpl. writeRawExpressionData(ExpressionExperiment ee, QuantitationType qt, Writer writer)
void
ExpressionDataFileServiceImpl. writeTsv(ExpressionExperiment entity, Writer writer)
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Uses of ExpressionExperiment in ubic.gemma.core.annotation.reference
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Uses of ExpressionExperiment in ubic.gemma.core.apps
Methods in ubic.gemma.core.apps that return ExpressionExperiment Modifier and Type Method Description protected ExpressionExperiment
ExperimentalDesignImportCli. locateExpressionExperiment(String shortName)
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Uses of ExpressionExperiment in ubic.gemma.core.datastructure.matrix
Methods in ubic.gemma.core.datastructure.matrix that return ExpressionExperiment Modifier and Type Method Description ExpressionExperiment
BaseExpressionDataMatrix. getExpressionExperiment()
The associatedExpressionExperiment
, if known.ExpressionExperiment
ExpressionDataMatrix. getExpressionExperiment()
Return the expression experiment this matrix is holding data for.Methods in ubic.gemma.core.datastructure.matrix with parameters of type ExpressionExperiment Modifier and Type Method Description static void
ExpressionDataWriterUtils. appendBaseHeader(ExpressionExperiment experiment, boolean design, StringBuffer buf)
Appends base header information (about the experiment) to a file.static void
ExpressionDataWriterUtils. appendBaseHeader(ExpressionExperiment experiment, String fileTypeStr, StringBuffer buf)
Appends base header information (about the experiment) to a file.void
ExperimentalDesignWriter. write(Writer writer, ExpressionExperiment ee, boolean writeHeader)
void
ExperimentalDesignWriter. write(Writer writer, ExpressionExperiment ee, Collection<BioAssay> bioAssays, boolean writeBaseHeader, boolean writeHeader)
Constructors in ubic.gemma.core.datastructure.matrix with parameters of type ExpressionExperiment Constructor Description ExpressionDataDoubleMatrix(ExpressionExperiment ee, QuantitationType qt, DoubleMatrix<CompositeSequence,BioMaterial> matrix)
Create a matrix given a 'raw' matrix that uses the same samples as the experiment.ExpressionDataStringMatrix(ExpressionExperiment expressionExperiment, Collection<CompositeSequence> designElements, QuantitationType quantitationType)
ExpressionDataStringMatrix(ExpressionExperiment expressionExperiment, QuantitationType quantitationType)
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Uses of ExpressionExperiment in ubic.gemma.core.expression.experiment
Methods in ubic.gemma.core.expression.experiment with parameters of type ExpressionExperiment Modifier and Type Method Description String
ExpressionExperimentMetaFileType. getDownloadName(ExpressionExperiment ee)
String
ExpressionExperimentMetaFileType. getFileName(ExpressionExperiment ee)
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Uses of ExpressionExperiment in ubic.gemma.core.loader.entrez.pubmed
Methods in ubic.gemma.core.loader.entrez.pubmed with parameters of type ExpressionExperiment Modifier and Type Method Description BibliographicReference
ExpressionExperimentBibRefFinder. locatePrimaryReference(ExpressionExperiment ee)
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Uses of ExpressionExperiment in ubic.gemma.core.loader.expression
Methods in ubic.gemma.core.loader.expression that return ExpressionExperiment Modifier and Type Method Description ExpressionExperiment
DataUpdater. addData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)
ExpressionExperiment
DataUpdaterImpl. addData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)
Generic but in practice used for RNA-seq.ExpressionExperiment
DataUpdater. replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)
ExpressionExperiment
DataUpdaterImpl. replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)
Replace the data associated with the experiment (or add it if there is none).Methods in ubic.gemma.core.loader.expression with parameters of type ExpressionExperiment Modifier and Type Method Description void
DataUpdater. addAffyDataFromAPTOutput(ExpressionExperiment ee, String pathToAptOutputFile)
void
DataUpdaterImpl. addAffyDataFromAPTOutput(ExpressionExperiment ee, String pathToAptOutputFile)
Affymetrix: Use to bypass the automated running of apt-probeset-summarize.void
DataUpdater. addCountData(ExpressionExperiment ee, ArrayDesign targetArrayDesign, DoubleMatrix<String,String> countMatrix, DoubleMatrix<String,String> rpkmMatrix, Integer readLength, Boolean isPairedReads, boolean allowMissingSamples)
void
DataUpdaterImpl. addCountData(ExpressionExperiment ee, ArrayDesign targetArrayDesign, DoubleMatrix<String,String> countMatrix, DoubleMatrix<String,String> rpkmMatrix, Integer readLength, Boolean isPairedReads, boolean allowMissingSamples)
RNA-seq: Replaces data.ExpressionExperiment
DataUpdater. addData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)
ExpressionExperiment
DataUpdaterImpl. addData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)
Generic but in practice used for RNA-seq.void
DataUpdater. log2cpmFromCounts(ExpressionExperiment ee, QuantitationType qt)
void
DataUpdaterImpl. log2cpmFromCounts(ExpressionExperiment ee, QuantitationType qt)
RNA-seq: For back filling log2cpm when only counts are available.void
ExperimentPlatformSwitchHelperService. persist(ExpressionExperiment expExp, ArrayDesign arrayDesign)
ExpressionExperiment
DataUpdater. replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)
void
DataUpdater. replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, QuantitationType qt, DoubleMatrix<String,String> data)
ExpressionExperiment
DataUpdaterImpl. replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)
Replace the data associated with the experiment (or add it if there is none).void
DataUpdaterImpl. replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, QuantitationType qt, DoubleMatrix<String,String> data)
Replace the data associated with the experiment (or add it if there is none).void
DataUpdater. reprocessAffyDataFromCel(ExpressionExperiment ee)
void
DataUpdaterImpl. reprocessAffyDataFromCel(ExpressionExperiment ee)
Affymetrix only: Provide or replace data for an Affymetrix-based experiment, using CEL files.void
ExpressionExperimentPlatformSwitchService. switchExperimentToArrayDesign(ExpressionExperiment ee, ArrayDesign arrayDesign)
If you know the array designs are already in a merged state, you should use switchExperimentToMergedPlatformArrayDesign
ExpressionExperimentPlatformSwitchService. switchExperimentToMergedPlatform(ExpressionExperiment expExp)
Automatically identify an appropriate merged platform -
Uses of ExpressionExperiment in ubic.gemma.core.loader.expression.arrayDesign
Methods in ubic.gemma.core.loader.expression.arrayDesign with parameters of type ExpressionExperiment Modifier and Type Method Description static Map<BioAssay,String>
AffyChipTypeExtractor. getChipTypes(ExpressionExperiment ee, Collection<LocalFile> files)
Extract a string like "Rat230_2" from CEL files. -
Uses of ExpressionExperiment in ubic.gemma.core.loader.expression.geo
Methods in ubic.gemma.core.loader.expression.geo with parameters of type ExpressionExperiment Modifier and Type Method Description void
GeoConverter. convertSubsetToExperimentalFactor(ExpressionExperiment expExp, GeoSubset geoSubSet)
Converts Geo subsets to experimental factors.void
GeoConverterImpl. convertSubsetToExperimentalFactor(ExpressionExperiment expExp, GeoSubset geoSubSet)
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Uses of ExpressionExperiment in ubic.gemma.core.loader.expression.simple
Methods in ubic.gemma.core.loader.expression.simple that return ExpressionExperiment Modifier and Type Method Description ExpressionExperiment
SimpleExpressionDataLoaderService. convert(SimpleExpressionExperimentMetaData metaData, DoubleMatrix<String,String> matrix)
ExpressionExperiment
SimpleExpressionDataLoaderServiceImpl. convert(SimpleExpressionExperimentMetaData metaData, DoubleMatrix<String,String> matrix)
ExpressionExperiment
SimpleExpressionDataLoaderService. create(SimpleExpressionExperimentMetaData metaData, InputStream data)
Parses, converts (into Gemma objects), and loads data into the database.ExpressionExperiment
SimpleExpressionDataLoaderServiceImpl. create(SimpleExpressionExperimentMetaData metaData, InputStream data)
Methods in ubic.gemma.core.loader.expression.simple with parameters of type ExpressionExperiment Modifier and Type Method Description void
ExperimentalDesignImporter. importDesign(ExpressionExperiment experiment, InputStream is)
This is the main builder director method of the application: It processes the input file containing information about the experimental design for a given expression experiment.void
ExperimentalDesignImporterImpl. importDesign(ExpressionExperiment experiment, InputStream is)
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Uses of ExpressionExperiment in ubic.gemma.core.search
Methods in ubic.gemma.core.search that return types with arguments of type ExpressionExperiment Modifier and Type Method Description default Collection<SearchResult<ExpressionExperiment>>
SearchSource. searchExpressionExperiment(SearchSettings settings)
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Uses of ExpressionExperiment in ubic.gemma.core.search.source
Methods in ubic.gemma.core.search.source that return types with arguments of type ExpressionExperiment Modifier and Type Method Description Collection<SearchResult<ExpressionExperiment>>
CompositeSearchSource. searchExpressionExperiment(SearchSettings settings)
Collection<SearchResult<ExpressionExperiment>>
DatabaseSearchSource. searchExpressionExperiment(SearchSettings settings)
Does search on exact string by: id, name and short name.Collection<SearchResult<ExpressionExperiment>>
HibernateSearchSource. searchExpressionExperiment(SearchSettings settings)
Collection<SearchResult<ExpressionExperiment>>
OntologySearchSource. searchExpressionExperiment(SearchSettings settings)
Search via characteristics i.e. -
Uses of ExpressionExperiment in ubic.gemma.core.tasks.analysis.coexp
Methods in ubic.gemma.core.tasks.analysis.coexp that return ExpressionExperiment Modifier and Type Method Description ExpressionExperiment
LinkAnalysisTaskCommand. getExpressionExperiment()
Methods in ubic.gemma.core.tasks.analysis.coexp with parameters of type ExpressionExperiment Modifier and Type Method Description void
LinkAnalysisTaskCommand. setExpressionExperiment(ExpressionExperiment expressionExperiment)
Constructors in ubic.gemma.core.tasks.analysis.coexp with parameters of type ExpressionExperiment Constructor Description LinkAnalysisTaskCommand(ExpressionExperiment ee, LinkAnalysisConfig lac, FilterConfig fg)
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Uses of ExpressionExperiment in ubic.gemma.core.tasks.analysis.diffex
Methods in ubic.gemma.core.tasks.analysis.diffex that return ExpressionExperiment Modifier and Type Method Description ExpressionExperiment
DifferentialExpressionAnalysisTaskCommand. getExpressionExperiment()
Methods in ubic.gemma.core.tasks.analysis.diffex with parameters of type ExpressionExperiment Modifier and Type Method Description void
DifferentialExpressionAnalysisTaskCommand. setExpressionExperiment(ExpressionExperiment expressionExperiment)
Constructors in ubic.gemma.core.tasks.analysis.diffex with parameters of type ExpressionExperiment Constructor Description DifferentialExpressionAnalysisRemoveTaskCommand(ExpressionExperiment ee, DifferentialExpressionAnalysis toRemove)
DifferentialExpressionAnalysisTaskCommand(String taskId, boolean forceAnalysis, ExpressionExperiment expressionExperiment)
DifferentialExpressionAnalysisTaskCommand(ExpressionExperiment ee)
DifferentialExpressionAnalysisTaskCommand(ExpressionExperiment ee, DifferentialExpressionAnalysis toRedo)
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Uses of ExpressionExperiment in ubic.gemma.core.tasks.analysis.expression
Methods in ubic.gemma.core.tasks.analysis.expression that return ExpressionExperiment Modifier and Type Method Description ExpressionExperiment
PreprocessTaskCommand. getExpressionExperiment()
ExpressionExperiment
SvdTaskCommand. getExpressionExperiment()
ExpressionExperiment
TwoChannelMissingValueTaskCommand. getExpressionExperiment()
Methods in ubic.gemma.core.tasks.analysis.expression with parameters of type ExpressionExperiment Modifier and Type Method Description void
PreprocessTaskCommand. setExpressionExperiment(ExpressionExperiment expressionExperiment)
void
SvdTaskCommand. setExpressionExperiment(ExpressionExperiment expressionExperiment)
void
TwoChannelMissingValueTaskCommand. setExpressionExperiment(ExpressionExperiment expressionExperiment)
Constructors in ubic.gemma.core.tasks.analysis.expression with parameters of type ExpressionExperiment Constructor Description BatchInfoFetchTaskCommand(ExpressionExperiment expressionExperiment)
PreprocessTaskCommand(ExpressionExperiment ee)
SvdTaskCommand(ExpressionExperiment expressionExperiment)
SvdTaskCommand(ExpressionExperiment expressionExperiment, boolean postProcessOnly)
TwoChannelMissingValueTaskCommand(ExpressionExperiment ee)
TwoChannelMissingValueTaskCommand(ExpressionExperiment expressionExperiment, double s2n, Collection<Double> extraMissingValueIndictors)
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Uses of ExpressionExperiment in ubic.gemma.core.tasks.maintenance
Methods in ubic.gemma.core.tasks.maintenance that return ExpressionExperiment Modifier and Type Method Description ExpressionExperiment
ExpressionExperimentReportTaskCommand. getExpressionExperiment()
Methods in ubic.gemma.core.tasks.maintenance with parameters of type ExpressionExperiment Modifier and Type Method Description void
ExpressionExperimentReportTaskCommand. setExpressionExperiment(ExpressionExperiment expressionExperiment)
Constructors in ubic.gemma.core.tasks.maintenance with parameters of type ExpressionExperiment Constructor Description ExpressionExperimentReportTaskCommand(ExpressionExperiment expressionExperiment)
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Uses of ExpressionExperiment in ubic.gemma.core.visualization
Methods in ubic.gemma.core.visualization with parameters of type ExpressionExperiment Modifier and Type Method Description protected void
ExperimentalDesignVisualizationServiceImpl. plotExperimentalDesign(ExpressionExperiment e)
Test method for now, shows how this can be used. -
Uses of ExpressionExperiment in ubic.gemma.model.common.quantitationtype
Constructors in ubic.gemma.model.common.quantitationtype with parameters of type ExpressionExperiment Constructor Description QuantitationTypeValueObject(QuantitationType qt, ExpressionExperiment expressionExperiment, Class<? extends DesignElementDataVector> vectorType)
Create aQuantitationType
VO in the context of an associated experiment. -
Uses of ExpressionExperiment in ubic.gemma.model.expression.bioAssayData
Methods in ubic.gemma.model.expression.bioAssayData that return ExpressionExperiment Modifier and Type Method Description abstract ExpressionExperiment
DesignElementDataVector. getExpressionExperiment()
ExpressionExperiment
ProcessedExpressionDataVector. getExpressionExperiment()
ExpressionExperiment
RawExpressionDataVector. getExpressionExperiment()
Methods in ubic.gemma.model.expression.bioAssayData with parameters of type ExpressionExperiment Modifier and Type Method Description abstract void
DesignElementDataVector. setExpressionExperiment(ExpressionExperiment expressionExperiment)
void
ProcessedExpressionDataVector. setExpressionExperiment(ExpressionExperiment expressionExperiment)
void
RawExpressionDataVector. setExpressionExperiment(ExpressionExperiment expressionExperiment)
void
MeanVarianceRelation. setSecurityOwner(ExpressionExperiment ee)
DesignElementDataVector
DoubleVectorValueObject. toDesignElementDataVector(ExpressionExperiment ee, CompositeSequence cs, QuantitationType updatedQuantitationType)
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Uses of ExpressionExperiment in ubic.gemma.model.expression.experiment
Methods in ubic.gemma.model.expression.experiment that return ExpressionExperiment Modifier and Type Method Description ExpressionExperiment
FactorValue. getSecurityOwner()
ExpressionExperiment
ExpressionExperimentSubSet. getSourceExperiment()
static ExpressionExperiment
ExpressionExperiment.Factory. newInstance()
Methods in ubic.gemma.model.expression.experiment that return types with arguments of type ExpressionExperiment Modifier and Type Method Description Set<ExpressionExperiment>
ExpressionExperiment. getOtherParts()
Methods in ubic.gemma.model.expression.experiment with parameters of type ExpressionExperiment Modifier and Type Method Description void
ExperimentalFactor. setSecurityOwner(ExpressionExperiment securityOwner)
void
FactorValue. setSecurityOwner(ExpressionExperiment ee)
void
ExpressionExperimentSubSet. setSourceExperiment(ExpressionExperiment sourceExperiment)
Method parameters in ubic.gemma.model.expression.experiment with type arguments of type ExpressionExperiment Modifier and Type Method Description void
ExpressionExperiment. setOtherParts(Set<ExpressionExperiment> otherParts)
Constructors in ubic.gemma.model.expression.experiment with parameters of type ExpressionExperiment Constructor Description ExpressionExperimentDetailsValueObject(ExpressionExperiment ee)
ExpressionExperimentDetailsValueObject(ExpressionExperiment ee, gemma.gsec.acl.domain.AclObjectIdentity aoi, gemma.gsec.acl.domain.AclSid sid)
ExpressionExperimentValueObject(ExpressionExperiment ee)
ExpressionExperimentValueObject(ExpressionExperiment ee, boolean ignoreDesign, boolean ignoreAccession)
Creates a new value object out of given Expression Experiment.ExpressionExperimentValueObject(ExpressionExperiment ee, gemma.gsec.acl.domain.AclObjectIdentity aoi, gemma.gsec.acl.domain.AclSid sid)
Creates a newExpressionExperiment
value object with additional information about ownership. -
Uses of ExpressionExperiment in ubic.gemma.persistence.persister
Methods in ubic.gemma.persistence.persister that return ExpressionExperiment Modifier and Type Method Description ExpressionExperiment
ExpressionPersister. persist(ExpressionExperiment ee, ArrayDesignsForExperimentCache cachedArrays)
ExpressionExperiment
PersisterHelper. persist(ExpressionExperiment ee, ArrayDesignsForExperimentCache cachedArrays)
protected ExpressionExperiment
ExpressionPersister. persistExpressionExperiment(ExpressionExperiment ee, AbstractPersister.Caches caches)
Methods in ubic.gemma.persistence.persister with parameters of type ExpressionExperiment Modifier and Type Method Description ExpressionExperiment
ExpressionPersister. persist(ExpressionExperiment ee, ArrayDesignsForExperimentCache cachedArrays)
ExpressionExperiment
PersisterHelper. persist(ExpressionExperiment ee, ArrayDesignsForExperimentCache cachedArrays)
protected ExpressionExperiment
ExpressionPersister. persistExpressionExperiment(ExpressionExperiment ee, AbstractPersister.Caches caches)
ArrayDesignsForExperimentCache
ExpressionPersister. prepare(ExpressionExperiment ee)
ArrayDesignsForExperimentCache
PersisterHelper. prepare(ExpressionExperiment ee)
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Uses of ExpressionExperiment in ubic.gemma.persistence.service
Methods in ubic.gemma.persistence.service with parameters of type ExpressionExperiment Modifier and Type Method Description ArrayDesignsForExperimentCache
ExpressionExperimentPrePersistService. prepare(ExpressionExperiment ee)
Call this before calling the persister.ArrayDesignsForExperimentCache
ExpressionExperimentPrePersistService. prepare(ExpressionExperiment ee, ArrayDesignsForExperimentCache c)
ArrayDesignsForExperimentCache
ExpressionExperimentPrePersistServiceImpl. prepare(ExpressionExperiment ee)
ArrayDesignsForExperimentCache
ExpressionExperimentPrePersistServiceImpl. prepare(ExpressionExperiment ee, ArrayDesignsForExperimentCache cache)
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Uses of ExpressionExperiment in ubic.gemma.persistence.service.analysis.expression
Methods in ubic.gemma.persistence.service.analysis.expression that return types with arguments of type ExpressionExperiment Modifier and Type Method Description Collection<ExpressionExperiment>
ExpressionExperimentSetDao. getExperimentsInSet(Long id)
Collection<ExpressionExperiment>
ExpressionExperimentSetDaoImpl. getExperimentsInSet(Long id)
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Uses of ExpressionExperiment in ubic.gemma.persistence.service.analysis.expression.coexpression
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Uses of ExpressionExperiment in ubic.gemma.persistence.service.analysis.expression.diff
Methods in ubic.gemma.persistence.service.analysis.expression.diff that return types with arguments of type ExpressionExperiment Modifier and Type Method Description 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)
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Uses of ExpressionExperiment in ubic.gemma.persistence.service.analysis.expression.pca
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Uses of ExpressionExperiment in ubic.gemma.persistence.service.analysis.expression.sampleCoexpression
Methods in ubic.gemma.persistence.service.analysis.expression.sampleCoexpression with parameters of type ExpressionExperiment Modifier and Type Method Description DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisService. compute(ExpressionExperiment ee, PreparedCoexMatrices matrices)
Computes sample correlation matrices for the given experiment.DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisServiceImpl. compute(ExpressionExperiment ee, PreparedCoexMatrices matrices)
Unfortunately, this method breaks under high contention (see #400, so we need to fully lock the database while undergoing usingIsolation.SERIALIZABLE
transaction isolation level.boolean
SampleCoexpressionAnalysisService. hasAnalysis(ExpressionExperiment ee)
boolean
SampleCoexpressionAnalysisServiceImpl. hasAnalysis(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisService. loadBestMatrix(ExpressionExperiment ee)
Loads the analysis containing the coexpression matrices for the given experiment and converts the regressed coexpression matrix into a double matrix.DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisServiceImpl. loadBestMatrix(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisService. loadFullMatrix(ExpressionExperiment ee)
Loads the analysis containing the coexpression matrices for the given experiment and converts the full (non-regressed) coexpression matrix into a double matrix.DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisServiceImpl. loadFullMatrix(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisService. loadRegressedMatrix(ExpressionExperiment ee)
Load the regressed coexpression matrix for the given experiment.DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisServiceImpl. loadRegressedMatrix(ExpressionExperiment ee)
PreparedCoexMatrices
SampleCoexpressionAnalysisService. prepare(ExpressionExperiment ee)
PreparedCoexMatrices
SampleCoexpressionAnalysisServiceImpl. prepare(ExpressionExperiment ee)
void
SampleCoexpressionAnalysisService. removeForExperiment(ExpressionExperiment ee)
Removes all coexpression matrices for the given experiment.void
SampleCoexpressionAnalysisServiceImpl. removeForExperiment(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisService. retrieveExisting(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisServiceImpl. retrieveExisting(ExpressionExperiment ee)
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Uses of ExpressionExperiment in ubic.gemma.persistence.service.common.description
Methods in ubic.gemma.persistence.service.common.description that return types with arguments of type ExpressionExperiment Modifier and Type Method Description Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>
CharacteristicDao. findExperimentReferencesByUris(Collection<String> uris, Taxon taxon, int limit, boolean rankByLevel)
Similar toCharacteristicDao.findExperimentsByUris(Collection, Taxon, int, boolean)
, but returns proxies with instead of initializing all the EEs in bulk.Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>
CharacteristicDaoImpl. findExperimentReferencesByUris(Collection<String> uris, Taxon taxon, int limit, boolean rankByLevel)
Since proxies are returned, they cannot be collected in aHashSet
which would otherwise cause their initialization by accessingObject.hashCode()
.Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>
CharacteristicDao. findExperimentsByUris(Collection<String> uris, Taxon taxon, int limit, boolean rankByLevel)
This search looks at direct annotations, factor values and biomaterials in that order.Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>
CharacteristicDaoImpl. findExperimentsByUris(Collection<String> uris, Taxon taxon, int limit, boolean rankByLevel)
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>
CharacteristicService. findExperimentsByUris(Collection<String> uris, Taxon taxon, int limit, boolean loadEEs, boolean rankByLevel)
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>
CharacteristicServiceImpl. findExperimentsByUris(Collection<String> uris, Taxon taxon, int limit, boolean loadEEs, boolean rankByLevel)
Map<ExpressionExperiment,BibliographicReference>
BibliographicReferenceDao. getAllExperimentLinkedReferences()
Map<ExpressionExperiment,BibliographicReference>
BibliographicReferenceDaoImpl. getAllExperimentLinkedReferences()
Map<BibliographicReference,Collection<ExpressionExperiment>>
BibliographicReferenceDao. getRelatedExperiments(Collection<BibliographicReference> records)
Map<BibliographicReference,Collection<ExpressionExperiment>>
BibliographicReferenceDaoImpl. getRelatedExperiments(Collection<BibliographicReference> records)
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Uses of ExpressionExperiment in ubic.gemma.persistence.service.common.quantitationtype
Methods in ubic.gemma.persistence.service.common.quantitationtype with parameters of type ExpressionExperiment Modifier and Type Method Description boolean
QuantitationTypeDao. existsByExpressionExperimentAndVectorType(QuantitationType quantitationType, ExpressionExperiment ee, Class<? extends DesignElementDataVector> dataVectorClass)
Test if a given quantitation type is used by a given experiment for a given vector type.boolean
QuantitationTypeDaoImpl. existsByExpressionExperimentAndVectorType(QuantitationType quantitationType, ExpressionExperiment ee, Class<? extends DesignElementDataVector> dataVectorClass)
boolean
QuantitationTypeService. existsByExpressionExperimentAndVectorType(QuantitationType quantitationType, ExpressionExperiment ee, Class<? extends DesignElementDataVector> dataVectorType)
Find a quantitation type by ID and vector type.boolean
QuantitationTypeServiceImpl. existsByExpressionExperimentAndVectorType(QuantitationType quantitationType, ExpressionExperiment ee, Class<? extends DesignElementDataVector> dataVectorType)
QuantitationType
QuantitationTypeDao. find(ExpressionExperiment ee, QuantitationType quantitationType)
Locate a QT associated with the given ee matching the specification of the passed quantitationType, or null if there isn't one.QuantitationType
QuantitationTypeDaoImpl. find(ExpressionExperiment ee, QuantitationType quantitationType)
QuantitationType
QuantitationTypeService. find(ExpressionExperiment ee, QuantitationType quantitationType)
Locate a QT associated with the given ee matching the specification of the passed quantitationType, or null if there isn't one.QuantitationType
QuantitationTypeServiceImpl. find(ExpressionExperiment ee, QuantitationType quantitationType)
List<QuantitationTypeValueObject>
QuantitationTypeDao. loadValueObjectsWithExpressionExperiment(Collection<QuantitationType> qts, ExpressionExperiment ee)
List<QuantitationTypeValueObject>
QuantitationTypeDaoImpl. loadValueObjectsWithExpressionExperiment(Collection<QuantitationType> qts, ExpressionExperiment ee)
LoadQuantitationTypeValueObject
in the context of an associated expression experiment.List<QuantitationTypeValueObject>
QuantitationTypeService. loadValueObjectsWithExpressionExperiment(Collection<QuantitationType> qts, ExpressionExperiment expressionExperiment)
List<QuantitationTypeValueObject>
QuantitationTypeServiceImpl. loadValueObjectsWithExpressionExperiment(Collection<QuantitationType> qts, ExpressionExperiment expressionExperiment)
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Uses of ExpressionExperiment in ubic.gemma.persistence.service.expression.arrayDesign
Methods in ubic.gemma.persistence.service.expression.arrayDesign that return types with arguments of type ExpressionExperiment Modifier and Type Method Description Collection<ExpressionExperiment>
ArrayDesignDao. getExpressionExperiments(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>
ArrayDesignDaoImpl. getExpressionExperiments(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>
ArrayDesignService. getExpressionExperiments(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>
ArrayDesignServiceImpl. getExpressionExperiments(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>
ArrayDesignService. getSwitchedExperiments(ArrayDesign id)
Get the ids of experiments that "originally" used this platform, but which don't any more due to a platform switch.Collection<ExpressionExperiment>
ArrayDesignServiceImpl. getSwitchedExperiments(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>
ArrayDesignDao. getSwitchedExpressionExperiments(ArrayDesign arrayDesign)
Obtain a collection ofExpressionExperiment
identifiers that have been switched from a given platform.Collection<ExpressionExperiment>
ArrayDesignDaoImpl. getSwitchedExpressionExperiments(ArrayDesign arrayDesign)
Get the ids of experiments that "originally" used this platform, but which don't any more due to a platform switch. -
Uses of ExpressionExperiment in ubic.gemma.persistence.service.expression.bioAssayData
Methods in ubic.gemma.persistence.service.expression.bioAssayData with parameters of type ExpressionExperiment Modifier and Type Method Description void
ProcessedExpressionDataVectorService. computeProcessedExpressionData(ExpressionExperiment ee)
Compute processed expression data, ignoring mismatched with the inferred scale.void
ProcessedExpressionDataVectorService. computeProcessedExpressionData(ExpressionExperiment ee, boolean ignoreInferredScale)
This method should not be called on its own, if possible.void
ProcessedExpressionDataVectorServiceImpl. computeProcessedExpressionData(ExpressionExperiment ee)
void
ProcessedExpressionDataVectorServiceImpl. computeProcessedExpressionData(ExpressionExperiment ee, boolean ignoreQuantitationMismatch)
Set<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorDao. createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean ignoreQuantitationMismatch)
Populate the processed data for the given experiment.Set<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorDaoImpl. createProcessedDataVectors(ExpressionExperiment ee, boolean ignoreQuantitationMismatch)
Set<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorService. createProcessedDataVectors(ExpressionExperiment expressionExperiment)
Set<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorService. createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean ignoreInferredScale)
Populate the processed data for the given experiment.Set<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorServiceImpl. createProcessedDataVectors(ExpressionExperiment expressionExperiment)
Set<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorServiceImpl. createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean ignoreQuantitationMismatch)
Collection<T>
AbstractDesignElementDataVectorDao. findByExpressionExperiment(ExpressionExperiment ee)
Collection<T>
DesignElementDataVectorDao. findByExpressionExperiment(ExpressionExperiment ee)
Collection<RawExpressionDataVector>
RawExpressionDataVectorDao. findByExpressionExperiment(ExpressionExperiment ee, QuantitationType quantitationType)
Collection<RawExpressionDataVector>
RawExpressionDataVectorDaoImpl. findByExpressionExperiment(ExpressionExperiment ee, QuantitationType quantitationType)
Collection<RawExpressionDataVector>
RawExpressionDataVectorService. findByExpressionExperiment(ExpressionExperiment ee, QuantitationType quantitationType)
Collection<RawExpressionDataVector>
RawExpressionDataVectorServiceImpl. findByExpressionExperiment(ExpressionExperiment ee, QuantitationType quantitationType)
Collection<DoubleVectorValueObject>
ProcessedExpressionDataVectorService. getProcessedDataArrays(ExpressionExperiment expressionExperiment)
Collection<DoubleVectorValueObject>
ProcessedExpressionDataVectorService. getProcessedDataArrays(ExpressionExperiment ee, int limit)
Collection<DoubleVectorValueObject>
ProcessedExpressionDataVectorServiceImpl. getProcessedDataArrays(ExpressionExperiment expressionExperiment)
Collection<DoubleVectorValueObject>
ProcessedExpressionDataVectorServiceImpl. getProcessedDataArrays(ExpressionExperiment ee, int limit)
Collection<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorService. getProcessedDataVectors(ExpressionExperiment expressionExperiment)
Collection<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorServiceImpl. getProcessedDataVectors(ExpressionExperiment expressionExperiment)
Collection<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorService. getProcessedDataVectorsAndThaw(ExpressionExperiment expressionExperiment)
Collection<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorServiceImpl. getProcessedDataVectorsAndThaw(ExpressionExperiment expressionExperiment)
Collection<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorDao. getProcessedVectors(ExpressionExperiment expressionExperiment)
Collection<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorDaoImpl. getProcessedVectors(ExpressionExperiment ee)
Map<Gene,Collection<Double>>
ProcessedExpressionDataVectorDao. getRanks(ExpressionExperiment expressionExperiment, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<CompositeSequence,Double>
ProcessedExpressionDataVectorDao. getRanks(ExpressionExperiment expressionExperiment, ProcessedExpressionDataVectorDao.RankMethod method)
Map<Gene,Collection<Double>>
ProcessedExpressionDataVectorDaoImpl. getRanks(ExpressionExperiment expressionExperiment, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<CompositeSequence,Double>
ProcessedExpressionDataVectorDaoImpl. getRanks(ExpressionExperiment expressionExperiment, ProcessedExpressionDataVectorDao.RankMethod method)
Map<Gene,Collection<Double>>
ProcessedExpressionDataVectorService. getRanks(ExpressionExperiment expressionExperiment, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<CompositeSequence,Double>
ProcessedExpressionDataVectorService. getRanks(ExpressionExperiment expressionExperiment, ProcessedExpressionDataVectorDao.RankMethod method)
Map<Gene,Collection<Double>>
ProcessedExpressionDataVectorServiceImpl. getRanks(ExpressionExperiment expressionExperiment, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<CompositeSequence,Double>
ProcessedExpressionDataVectorServiceImpl. getRanks(ExpressionExperiment expressionExperiment, ProcessedExpressionDataVectorDao.RankMethod method)
void
ProcessedExpressionDataVectorDao. removeProcessedDataVectors(ExpressionExperiment expressionExperiment)
void
ProcessedExpressionDataVectorDaoImpl. removeProcessedDataVectors(ExpressionExperiment expressionExperiment)
void
ProcessedExpressionDataVectorService. removeProcessedDataVectors(ExpressionExperiment expressionExperiment)
void
ProcessedExpressionDataVectorServiceImpl. removeProcessedDataVectors(ExpressionExperiment expressionExperiment)
void
ProcessedExpressionDataVectorService. reorderByDesign(ExpressionExperiment ee)
Creates new bioAssayDimensions to match the experimental design, reorders the data to match, updates.void
ProcessedExpressionDataVectorServiceImpl. reorderByDesign(ExpressionExperiment ee)
void
ProcessedExpressionDataVectorService. replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
Replace the processed vectors of a EE with the given vectors.void
ProcessedExpressionDataVectorServiceImpl. replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
void
ProcessedExpressionDataVectorService. updateRanks(ExpressionExperiment ee)
void
ProcessedExpressionDataVectorServiceImpl. updateRanks(ExpressionExperiment ee)
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Uses of ExpressionExperiment in ubic.gemma.persistence.service.expression.biomaterial
Methods in ubic.gemma.persistence.service.expression.biomaterial that return ExpressionExperiment Modifier and Type Method Description ExpressionExperiment
BioMaterialDao. getExpressionExperiment(Long bioMaterialId)
ExpressionExperiment
BioMaterialDaoImpl. getExpressionExperiment(Long bioMaterialId)
ExpressionExperiment
BioMaterialService. getExpressionExperiment(Long id)
ExpressionExperiment
BioMaterialServiceImpl. getExpressionExperiment(Long id)
Methods in ubic.gemma.persistence.service.expression.biomaterial with parameters of type ExpressionExperiment Modifier and Type Method Description Collection<BioMaterial>
BioMaterialDao. findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>
BioMaterialDaoImpl. findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>
BioMaterialService. findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>
BioMaterialServiceImpl. findByExperiment(ExpressionExperiment experiment)
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Uses of ExpressionExperiment in ubic.gemma.persistence.service.expression.experiment
Methods in ubic.gemma.persistence.service.expression.experiment with parameters of type ExpressionExperiment Modifier and Type Method Description void
ExpressionExperimentService. addCharacteristic(ExpressionExperiment ee, Characteristic vc)
Will add the vocab characteristic to the expression experiment and persist the changes.void
ExpressionExperimentServiceImpl. addCharacteristic(ExpressionExperiment ee, Characteristic vc)
Will add the characteristic to the expression experiment and persist the changes.ExperimentalFactor
ExpressionExperimentService. addFactor(ExpressionExperiment ee, ExperimentalFactor factor)
ExperimentalFactor
ExpressionExperimentServiceImpl. addFactor(ExpressionExperiment ee, ExperimentalFactor factor)
FactorValue
ExpressionExperimentService. addFactorValue(ExpressionExperiment ee, FactorValue fv)
FactorValue
ExpressionExperimentServiceImpl. addFactorValue(ExpressionExperiment ee, FactorValue fv)
Map<BioMaterial,FactorValue>
ExpressionExperimentService. addFactorValues(ExpressionExperiment ee, Map<BioMaterial,FactorValue> fvs)
Intended with the case of a continuous factor being added.Map<BioMaterial,FactorValue>
ExpressionExperimentServiceImpl. addFactorValues(ExpressionExperiment ee, Map<BioMaterial,FactorValue> fvs)
ExpressionExperiment
ExpressionExperimentService. addRawVectors(ExpressionExperiment eeToUpdate, Collection<RawExpressionDataVector> newVectors)
Used when we want to add data for a quantitation type.ExpressionExperiment
ExpressionExperimentServiceImpl. addRawVectors(ExpressionExperiment ee, Collection<RawExpressionDataVector> newVectors)
BlacklistedExperiment
BlacklistedEntityService. blacklistExpressionExperiment(ExpressionExperiment dataset, String reason)
Blacklist a given dataset.BlacklistedExperiment
BlacklistedEntityServiceImpl. blacklistExpressionExperiment(ExpressionExperiment dataset, String reason)
Geeq
GeeqService. calculateScore(ExpressionExperiment ee, GeeqService.ScoreMode mode)
Calculates the GEEQ score in the given mode for the experiment with the given id.Geeq
GeeqServiceImpl. calculateScore(ExpressionExperiment ee, GeeqService.ScoreMode mode)
BatchInformationFetchingEvent
ExpressionExperimentService. checkBatchFetchStatus(ExpressionExperiment ee)
BatchInformationFetchingEvent
ExpressionExperimentServiceImpl. checkBatchFetchStatus(ExpressionExperiment ee)
boolean
ExpressionExperimentService. checkHasBatchInfo(ExpressionExperiment ee)
boolean
ExpressionExperimentServiceImpl. checkHasBatchInfo(ExpressionExperiment ee)
protected ExpressionExperimentValueObject
ExpressionExperimentDaoImpl. doLoadValueObject(ExpressionExperiment entity)
ExpressionExperiment
ExpressionExperimentDaoImpl. find(ExpressionExperiment entity)
Map<Class<? extends Identifiable>,List<Characteristic>>
ExpressionExperimentDao. getAllAnnotations(ExpressionExperiment expressionExperiment)
Obtain all annotations, grouped by applicable level.Map<Class<? extends Identifiable>,List<Characteristic>>
ExpressionExperimentDaoImpl. getAllAnnotations(ExpressionExperiment expressionExperiment)
String
ExpressionExperimentService. getBatchConfound(ExpressionExperiment ee)
Checks the experiment for a batch confound.String
ExpressionExperimentServiceImpl. getBatchConfound(ExpressionExperiment ee)
BatchEffectType
ExpressionExperimentService. getBatchEffect(ExpressionExperiment ee)
Obtain aBatchEffectType
describing the batch effect state of the given experiment.BatchEffectType
ExpressionExperimentServiceImpl. getBatchEffect(ExpressionExperiment ee)
BatchEffectDetails
ExpressionExperimentService. getBatchEffectDetails(ExpressionExperiment ee)
Obtain the full batch effect details of a given experiment.BatchEffectDetails
ExpressionExperimentServiceImpl. getBatchEffectDetails(ExpressionExperiment ee)
String
ExpressionExperimentService. getBatchEffectStatistics(ExpressionExperiment ee)
Obtain a string describing the summary statistics of a batch effect is present in the given experiment.String
ExpressionExperimentServiceImpl. getBatchEffectStatistics(ExpressionExperiment ee)
Collection<BioAssayDimension>
ExpressionExperimentDao. getBioAssayDimensions(ExpressionExperiment expressionExperiment)
Collection<BioAssayDimension>
ExpressionExperimentDaoImpl. getBioAssayDimensions(ExpressionExperiment expressionExperiment)
Collection<BioAssayDimension>
ExpressionExperimentService. getBioAssayDimensions(ExpressionExperiment expressionExperiment)
Collection<BioAssayDimension>
ExpressionExperimentServiceImpl. getBioAssayDimensions(ExpressionExperiment expressionExperiment)
List<Characteristic>
ExpressionExperimentDao. getBioMaterialAnnotations(ExpressionExperiment expressionExperiment)
Obtain sample-level annotations.List<Characteristic>
ExpressionExperimentDaoImpl. getBioMaterialAnnotations(ExpressionExperiment expressionExperiment)
long
ExpressionExperimentDao. getBioMaterialCount(ExpressionExperiment expressionExperiment)
long
ExpressionExperimentDaoImpl. getBioMaterialCount(ExpressionExperiment expressionExperiment)
long
ExpressionExperimentService. getBioMaterialCount(ExpressionExperiment expressionExperiment)
long
ExpressionExperimentServiceImpl. getBioMaterialCount(ExpressionExperiment expressionExperiment)
long
ExpressionExperimentDao. getDesignElementDataVectorCount(ExpressionExperiment ee)
long
ExpressionExperimentDaoImpl. getDesignElementDataVectorCount(ExpressionExperiment ee)
long
ExpressionExperimentService. getDesignElementDataVectorCount(ExpressionExperiment ee)
long
ExpressionExperimentServiceImpl. getDesignElementDataVectorCount(ExpressionExperiment ee)
List<Characteristic>
ExpressionExperimentDao. getExperimentalDesignAnnotations(ExpressionExperiment expressionExperiment)
Obtain experimental design-level annotations.List<Characteristic>
ExpressionExperimentDaoImpl. getExperimentalDesignAnnotations(ExpressionExperiment expressionExperiment)
List<Characteristic>
ExpressionExperimentDao. getExperimentAnnotations(ExpressionExperiment expressionExperiment)
Obtain experiment-level annotations.List<Characteristic>
ExpressionExperimentDaoImpl. getExperimentAnnotations(ExpressionExperiment expressionExperiment)
Date
ExpressionExperimentDao. getLastArrayDesignUpdate(ExpressionExperiment ee)
Date
ExpressionExperimentDaoImpl. getLastArrayDesignUpdate(ExpressionExperiment ee)
Date
ExpressionExperimentService. getLastArrayDesignUpdate(ExpressionExperiment expressionExperiment)
Date
ExpressionExperimentServiceImpl. getLastArrayDesignUpdate(ExpressionExperiment ee)
QuantitationType
ExpressionExperimentDao. getPreferredQuantitationType(ExpressionExperiment ee)
Obtain the preferred quantitation type, if available.QuantitationType
ExpressionExperimentDaoImpl. getPreferredQuantitationType(ExpressionExperiment ee)
QuantitationType
ExpressionExperimentService. getPreferredQuantitationType(ExpressionExperiment ee)
Iterates over the quantitation types for a given expression experiment and returns the preferred quantitation types.QuantitationType
ExpressionExperimentServiceImpl. getPreferredQuantitationType(ExpressionExperiment ee)
Map<QuantitationType,Long>
ExpressionExperimentDao. getQuantitationTypeCount(ExpressionExperiment ee)
Map<QuantitationType,Long>
ExpressionExperimentDaoImpl. getQuantitationTypeCount(ExpressionExperiment ee)
Map<QuantitationType,Long>
ExpressionExperimentService. getQuantitationTypeCount(ExpressionExperiment ee)
Map<QuantitationType,Long>
ExpressionExperimentServiceImpl. getQuantitationTypeCount(ExpressionExperiment ee)
Collection<QuantitationType>
ExpressionExperimentDao. getQuantitationTypes(ExpressionExperiment expressionExperiment)
Collection<QuantitationType>
ExpressionExperimentDaoImpl. getQuantitationTypes(ExpressionExperiment expressionExperiment)
Collection<QuantitationType>
ExpressionExperimentService. getQuantitationTypes(ExpressionExperiment expressionExperiment)
Collection<QuantitationType>
ExpressionExperimentServiceImpl. getQuantitationTypes(ExpressionExperiment expressionExperiment)
Collection<QuantitationTypeValueObject>
ExpressionExperimentService. getQuantitationTypeValueObjects(ExpressionExperiment expressionExperiment)
Load allQuantitationType
associated to an expression experiment as VOs.Collection<QuantitationTypeValueObject>
ExpressionExperimentServiceImpl. getQuantitationTypeValueObjects(ExpressionExperiment expressionExperiment)
Collection<ExpressionExperimentSubSet>
ExpressionExperimentDao. getSubSets(ExpressionExperiment expressionExperiment)
Collection<ExpressionExperimentSubSet>
ExpressionExperimentDaoImpl. getSubSets(ExpressionExperiment expressionExperiment)
Collection<ExpressionExperimentSubSet>
ExpressionExperimentService. getSubSets(ExpressionExperiment expressionExperiment)
Collection<ExpressionExperimentSubSet>
ExpressionExperimentServiceImpl. getSubSets(ExpressionExperiment expressionExperiment)
boolean
ExpressionExperimentDao. hasProcessedExpressionData(ExpressionExperiment ee)
Test if the dataset has preferred expression data vectors.boolean
ExpressionExperimentDaoImpl. hasProcessedExpressionData(ExpressionExperiment ee)
boolean
ExpressionExperimentService. hasProcessedExpressionData(ExpressionExperiment ee)
Test if the given experiment has processed data vectors.boolean
ExpressionExperimentServiceImpl. hasProcessedExpressionData(ExpressionExperiment ee)
protected void
ExpressionExperimentDaoImpl. initializeCachedFilteringResult(ExpressionExperiment ee)
boolean
BlacklistedEntityDao. isBlacklisted(ExpressionExperiment dataset)
boolean
BlacklistedEntityDaoImpl. isBlacklisted(ExpressionExperiment dataset)
boolean
BlacklistedEntityService. isBlacklisted(ExpressionExperiment dataset)
boolean
BlacklistedEntityServiceImpl. isBlacklisted(ExpressionExperiment dataset)
boolean
ExpressionExperimentService. isRNASeq(ExpressionExperiment expressionExperiment)
boolean
ExpressionExperimentServiceImpl. isRNASeq(ExpressionExperiment expressionExperiment)
Boolean
ExpressionExperimentService. isSuitableForDEA(ExpressionExperiment ee)
Boolean
ExpressionExperimentServiceImpl. isSuitableForDEA(ExpressionExperiment ee)
boolean
ExpressionExperimentService. isTroubled(ExpressionExperiment expressionExperiment)
Check if the dataset is either troubled or uses a troubled platform.boolean
ExpressionExperimentServiceImpl. isTroubled(ExpressionExperiment ee)
void
ExpressionExperimentDaoImpl. remove(ExpressionExperiment ee)
void
ExpressionExperimentServiceImpl. remove(ExpressionExperiment ee)
Deletes an experiment and all of its associated objects, including coexpression links.ExpressionExperiment
ExpressionExperimentService. replaceRawVectors(ExpressionExperiment ee, Collection<RawExpressionDataVector> vectors)
Used when we are replacing data, such as when converting an experiment from one platform to another.ExpressionExperiment
ExpressionExperimentServiceImpl. replaceRawVectors(ExpressionExperiment ee, Collection<RawExpressionDataVector> newVectors)
void
ExpressionExperimentDao. thaw(ExpressionExperiment expressionExperiment)
void
ExpressionExperimentDaoImpl. thaw(ExpressionExperiment expressionExperiment)
ExpressionExperiment
ExpressionExperimentService. thaw(ExpressionExperiment expressionExperiment)
ExpressionExperiment
ExpressionExperimentServiceImpl. thaw(ExpressionExperiment expressionExperiment)
void
ExpressionExperimentDao. thawBioAssays(ExpressionExperiment expressionExperiment)
void
ExpressionExperimentDaoImpl. thawBioAssays(ExpressionExperiment expressionExperiment)
ExpressionExperiment
ExpressionExperimentService. thawBioAssays(ExpressionExperiment expressionExperiment)
ExpressionExperiment
ExpressionExperimentServiceImpl. thawBioAssays(ExpressionExperiment expressionExperiment)
void
ExpressionExperimentDao. thawForFrontEnd(ExpressionExperiment expressionExperiment)
void
ExpressionExperimentDaoImpl. thawForFrontEnd(ExpressionExperiment expressionExperiment)
ExpressionExperiment
ExpressionExperimentService. thawLite(ExpressionExperiment expressionExperiment)
Partially thaw the expression experiment given - do not thaw the raw data.ExpressionExperiment
ExpressionExperimentServiceImpl. thawLite(ExpressionExperiment expressionExperiment)
ExpressionExperiment
ExpressionExperimentService. thawLiter(ExpressionExperiment expressionExperiment)
ExpressionExperiment
ExpressionExperimentServiceImpl. thawLiter(ExpressionExperiment expressionExperiment)
void
ExpressionExperimentDao. thawWithoutVectors(ExpressionExperiment expressionExperiment)
void
ExpressionExperimentDaoImpl. thawWithoutVectors(ExpressionExperiment ee)
MeanVarianceRelation
ExpressionExperimentDao. updateMeanVarianceRelation(ExpressionExperiment ee, MeanVarianceRelation mvr)
MeanVarianceRelation
ExpressionExperimentDaoImpl. updateMeanVarianceRelation(ExpressionExperiment ee, MeanVarianceRelation mvr)
MeanVarianceRelation
ExpressionExperimentService. updateMeanVarianceRelation(ExpressionExperiment ee, MeanVarianceRelation mvr)
MeanVarianceRelation
ExpressionExperimentServiceImpl. updateMeanVarianceRelation(ExpressionExperiment ee, MeanVarianceRelation mvr)
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Uses of ExpressionExperiment in ubic.gemma.persistence.util
Methods in ubic.gemma.persistence.util with parameters of type ExpressionExperiment Modifier and Type Method Description static Collection<ArrayDesign>
CommonQueries. getArrayDesignsUsed(ExpressionExperiment ee, Session session)
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Uses of ExpressionExperiment in ubic.gemma.rest
Constructor parameters in ubic.gemma.rest with type arguments of type ExpressionExperiment Constructor Description ExpressionExperimentWithSearchResultValueObject(ExpressionExperimentValueObject vo, SearchResult<ExpressionExperiment> result)
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Uses of ExpressionExperiment in ubic.gemma.rest.util.args
Methods in ubic.gemma.rest.util.args that return types with arguments of type ExpressionExperiment Modifier and Type Method Description List<SearchResult<ExpressionExperiment>>
DatasetArgService. getResultsForSearchQuery(QueryArg query, Highlighter highlighter)
Obtain the search results for a given query and highlighter.Methods in ubic.gemma.rest.util.args with parameters of type ExpressionExperiment Modifier and Type Method Description QuantitationType
QuantitationTypeArgService. getEntity(QuantitationTypeArg<?> quantitationTypeArg, ExpressionExperiment ee, Class<? extends DesignElementDataVector> vectorType)
Method parameters in ubic.gemma.rest.util.args with type arguments of type ExpressionExperiment Modifier and Type Method Description Filters
DatasetArgService. getFilters(FilterArg<ExpressionExperiment> filterArg)
Filters
DatasetArgService. getFilters(FilterArg<ExpressionExperiment> filterArg, Collection<OntologyTerm> mentionedTerm)
Sort
DatasetArgService. getSort(SortArg<ExpressionExperiment> sortArg)
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Uses of ExpressionExperiment in ubic.gemma.web.controller.expression.experiment
Methods in ubic.gemma.web.controller.expression.experiment with parameters of type ExpressionExperiment Modifier and Type Method Description static Collection<DesignMatrixRowValueObject>
DesignMatrixRowValueObject.Factory. getDesignMatrix(ExpressionExperiment expressionExperiment, boolean removeBatchFactor, boolean removeContinuous)
String
ExpressionExperimentController. getQCTagHTML(ExpressionExperiment ee)
Used to include the html for the qc table in an ext panel (without using a tag) (This method should probably be in a service?)static boolean
ExpressionExperimentQCUtils. hasNodeDegreeDistFile(ExpressionExperiment ee)
static boolean
ExpressionExperimentQCUtils. hasPvalueDistFiles(ExpressionExperiment ee)
static int
ExpressionExperimentQCUtils. numFactors(ExpressionExperiment expressionExperiment)
Method parameters in ubic.gemma.web.controller.expression.experiment with type arguments of type ExpressionExperiment Modifier and Type Method Description Collection<AnnotationValueObject>
ExpressionExperimentController. getAnnotation(EntityDelegator<ExpressionExperiment> e)
AJAXCollection<BioMaterialValueObject>
ExperimentalDesignController. getBioMaterials(EntityDelegator<ExpressionExperiment> e)
Collection<DesignMatrixRowValueObject>
ExpressionExperimentController. getDesignMatrixRows(EntityDelegator<ExpressionExperiment> e)
AJAXCollection<ExperimentalFactorValueObject>
ExpressionExperimentController. getExperimentalFactors(EntityDelegator<ExpressionExperiment> e)
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Uses of ExpressionExperiment in ubic.gemma.web.util
Methods in ubic.gemma.web.util with parameters of type ExpressionExperiment Modifier and Type Method Description static String
AnchorTagUtil. getExpressionExperimentLink(ExpressionExperiment ee, String link, javax.servlet.ServletContext servletContext)
static String
AnchorTagUtil. getExpressionExperimentUrl(ExpressionExperiment ee, javax.servlet.ServletContext servletContext)
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