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)

      • 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".

      • getBatchEffectStatistics

        @Nullable
public String getBatchEffectStatistics()

      • 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​(@Nullable
                             String batchConfound)

      • setBatchEffectStatistics

        public void setBatchEffectStatistics​(@Nullable
                                     String batchEffectStatistics)

      • 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

        @Nullable
public Taxon getTaxon()
        Taxon of this dataset.

        This is a denormalization to speed up queries. For the definitive taxon, look at the bioAssays.sampleUsed.sourceTaxon. It's possible that more than one distinct taxa can be found that way such experiments should eventually be split by taxon.

      • hashCode

        public int hashCode()
        Description copied from class: AbstractIdentifiable
        Important note: Never use the ID in the hashCode() implementation since it can be assigned when the object is persisted.
        Overrides:
        hashCode in class AbstractDescribable

      • equals

        public boolean equals​(Object object)
        Description copied from class: AbstractIdentifiable
        Important note: Two objects with the same class and non-null ID must be considered equal. If one or both IDs are nulls, the rest of the state can be used to determine equality.
        Specified by:
        equals in class AbstractIdentifiable