Package ubic.gemma.model.expression.experiment

Class ExpressionExperiment

java.lang.Object
ubic.gemma.model.common.AbstractIdentifiable
ubic.gemma.model.common.AbstractDescribable
ubic.gemma.model.common.auditAndSecurity.AbstractAuditable
ubic.gemma.model.analysis.Investigation
ubic.gemma.model.expression.experiment.BioAssaySet
ubic.gemma.model.expression.experiment.ExpressionExperiment
All Implemented Interfaces:
gemma.gsec.model.Securable, gemma.gsec.model.SecuredNotChild, Auditable, Curatable, Securable, SecuredNotChild, Describable, Identifiable
@Indexed public class ExpressionExperiment extends BioAssaySet implements SecuredNotChild, Curatable
Author:
paul

  • Field Details

  • Constructor Details

    • ExpressionExperiment

      public ExpressionExperiment()

  • Method Details

    • 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)

    • getId

      @DocumentId public Long getId()
      Specified by:
      getId in interface Identifiable
      Specified by:
      getId in interface gemma.gsec.model.Securable
      Overrides:
      getId in class AbstractIdentifiable

    • 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

    • getDescription

      @Field(store=YES) public String getDescription()
      Description copied from interface: Describable
      Obtain a human-readable description of the object
      Specified by:
      getDescription in interface Describable
      Overrides:
      getDescription in class AbstractDescribable

    • getBioAssays

      @IndexedEmbedded public Set<BioAssay> getBioAssays()
      Overrides:
      getBioAssays in class BioAssaySet

    • getAccession

      @Nullable @IndexedEmbedded public DatabaseEntry getAccession()

    • getPrimaryPublication

      @IndexedEmbedded public BibliographicReference getPrimaryPublication()
      Overrides:
      getPrimaryPublication in class Investigation
      Returns:
      The primary citable publication for this investigation.

    • 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

      @Nullable public String getBatchConfound()

    • getBatchEffect

      @Nullable public BatchEffectType getBatchEffect()

    • getBatchEffectStatistics

      @Nullable public String getBatchEffectStatistics()

    • getCurationDetails

      public CurationDetails getCurationDetails()
      Specified by:
      getCurationDetails in interface Curatable

    • getExperimentalDesign

      @Nullable @IndexedEmbedded public ExperimentalDesign getExperimentalDesign()

    • getGeeq

      @Nullable public Geeq getGeeq()

    • getMeanVarianceRelation

      @Nullable public MeanVarianceRelation getMeanVarianceRelation()

    • getMetadata

      @Nullable public String getMetadata()

    • getNumberOfDataVectors

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

    • getNumberOfCells

      @Nullable public Integer getNumberOfCells()

    • getOtherParts

      public Set<ExpressionExperiment> getOtherParts()

    • getProcessedExpressionDataVectors

      public Set<ProcessedExpressionDataVector> getProcessedExpressionDataVectors()

    • getQuantitationTypes

      public Set<QuantitationType> getQuantitationTypes()

    • getSingleCellExpressionDataVectors

      public Set<SingleCellExpressionDataVector> getSingleCellExpressionDataVectors()

    • getRawExpressionDataVectors

      public Set<RawExpressionDataVector> getRawExpressionDataVectors()

    • 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.

    • setAccession

      public void setAccession(@Nullable DatabaseEntry accession)

    • setBatchConfound

      public void setBatchConfound(@Nullable String batchConfound)

    • setBatchEffect

      public void setBatchEffect(@Nullable BatchEffectType batchEffect)

    • setBatchEffectStatistics

      public void setBatchEffectStatistics(@Nullable String batchEffectStatistics)

    • setCurationDetails

      public void setCurationDetails(CurationDetails curationDetails)
      Specified by:
      setCurationDetails in interface Curatable

    • setExperimentalDesign

      public void setExperimentalDesign(@Nullable ExperimentalDesign experimentalDesign)

    • setGeeq

      public void setGeeq(@Nullable Geeq geeq)

    • setMeanVarianceRelation

      public void setMeanVarianceRelation(@Nullable MeanVarianceRelation meanVarianceRelation)

    • setMetadata

      public void setMetadata(@Nullable String metadata)

    • setNumberOfDataVectors

      public void setNumberOfDataVectors(Integer numberOfDataVectors)

    • setNumberOfCells

      public void setNumberOfCells(@Nullable Integer numberOfCells)

    • setOtherParts

      public void setOtherParts(Set<ExpressionExperiment> otherParts)

    • setProcessedExpressionDataVectors

      public void setProcessedExpressionDataVectors(Set<ProcessedExpressionDataVector> processedExpressionDataVectors)

    • setQuantitationTypes

      public void setQuantitationTypes(Set<QuantitationType> quantitationTypes)

    • setSingleCellExpressionDataVectors

      public void setSingleCellExpressionDataVectors(Set<SingleCellExpressionDataVector> singleCellExpressionDataVectors)

    • 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.

    • setTaxon

      public void setTaxon(@Nullable Taxon 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

    • toString

      public String toString()
      Overrides:
      toString in class AbstractDescribable