Package ubic.gemma.model.expression.experiment

Class ExpressionExperiment

    • Constructor Detail

      • ExpressionExperiment

        public ExpressionExperiment()

    • Method Detail

      • getNumberOfSamples

        public Integer getNumberOfSamples()
        Returns:
        the number of samples (bioassays). If there are multiple platforms used, this number may not be the same as the actual number of biological samples. This is a denormalization to speed up queries; the definitive count is always from this.getBioAssays().size()

      • setNumberOfSamples

        public void setNumberOfSamples​(Integer numberofSamples)

      • equals

        public boolean equals​(Object object)
        Description copied from class: AbstractDescribable
        Returns true if the argument is an Describable instance and all identifiers for this entity equal the identifiers of the argument entity. Returns false otherwise.
        Overrides:
        equals in class AbstractDescribable

      • getName

        @Field(store=YES)
public String getName()
        Description copied from interface: Describable
        Obtain the name of an object is a possibly ambiguous human-readable identifier that need not be an external database reference.
        Specified by:
        getName in interface Describable
        Overrides:
        getName in class AbstractDescribable

      • getOtherRelevantPublications

        @IndexedEmbedded
public Set<BibliographicReference> getOtherRelevantPublications()
        Overrides:
        getOtherRelevantPublications in class Investigation
        Returns:
        A collection of other publications that are directly relevant to this investigation (e.g., use the same data but are not the primary publication for the investigation).

      • getCharacteristics

        @IndexedEmbedded(includePaths={"value","valueUri"})
public Set<Characteristic> getCharacteristics()
        Overrides:
        getCharacteristics in class Investigation
        Returns:
        Annotations that describe the experiment as a whole, for example "tumor" or "brain".

      • getBatchConfound

        public String getBatchConfound()

      • getBatchEffectStatistics

        public String getBatchEffectStatistics()

      • getExperimentalDesign

        @IndexedEmbedded
public ExperimentalDesign getExperimentalDesign()

      • getGeeq

        public Geeq getGeeq()

      • getMetadata

        public String getMetadata()

      • getNumberOfDataVectors

        public Integer getNumberOfDataVectors()
        Returns:
        The number of ProcessedExpressionDataVectors associated with this.

      • getShortName

        @Field(analyze=NO)
public String getShortName()
        Returns:
        A brief unique (but optional) human-readable name for the expression experiment. For example in the past we often used names like "alizadeh-lymphoma".

      • getSource

        public String getSource()
        Returns:
        string describing how the data was obtained (e.g. direct upload) if it was not from a Accesssion in an ExternalDatabase (e.g. GEO)

      • getAllCharacteristics

        public Set<Characteristic> getAllCharacteristics()
        Obtain all characteristics associated to this EE.

        This relationship is not managed by this entity, so you should only query it.

      • setBatchConfound

        public void setBatchConfound​(String batchConfound)

      • setBatchEffect

        public void setBatchEffect​(BatchEffectType batchEffect)

      • setBatchEffectStatistics

        public void setBatchEffectStatistics​(String batchEffectStatistics)

      • setExperimentalDesign

        public void setExperimentalDesign​(ExperimentalDesign experimentalDesign)

      • setGeeq

        public void setGeeq​(Geeq geeq)

      • setMeanVarianceRelation

        public void setMeanVarianceRelation​(MeanVarianceRelation meanVarianceRelation)

      • setMetadata

        public void setMetadata​(String metadata)

      • setNumberOfDataVectors

        public void setNumberOfDataVectors​(Integer numberOfDataVectors)

      • setQuantitationTypes

        public void setQuantitationTypes​(Set<QuantitationType> quantitationTypes)

      • setRawExpressionDataVectors

        public void setRawExpressionDataVectors​(Set<RawExpressionDataVector> rawExpressionDataVectors)

      • setShortName

        public void setShortName​(String shortName)

      • setSource

        public void setSource​(String source)

      • setAllCharacteristics

        public void setAllCharacteristics​(Set<Characteristic> allCharacteristics)

      • getTaxon

        public Taxon getTaxon()
        This is a denormalization to speed up queries. For the definitive taxon, look at the bioAssays -> sampleUsed -> sourceTaxon
        Returns:
        the associated taxon

      • setTaxon

        public void setTaxon​(Taxon taxon)