ExpressionExperiment (Gemma 1.29.4 API)

java.lang.Object
- ubic.gemma.model.common.AbstractDescribable
- - ubic.gemma.model.common.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, Serializable, Auditable, Curatable, Describable, Identifiable
```
public class ExpressionExperiment
extends BioAssaySet
implements gemma.gsec.model.SecuredNotChild, Curatable
```
Author:

paul

See Also:

Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class ExpressionExperiment.Factory

Nested Classes
Modifier and Type	Class and Description
`static class`	`ExpressionExperiment.Factory`

Constructor Summary

Constructors
Constructor and Description

ExpressionExperiment()

Constructors
Constructor and Description
`ExpressionExperiment()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`ExpressionExperimentValueObject`	`createValueObject()` Special use case.
`boolean`	`equals(Object object)` Returns `true` if the argument is an Describable instance and all identifiers for this entity equal the identifiers of the argument entity.
`String`	`getBatchConfound()`
`String`	`getBatchEffect()`
`CurationDetails`	`getCurationDetails()`
`ExperimentalDesign`	`getExperimentalDesign()`
`Geeq`	`getGeeq()`
`MeanVarianceRelation`	`getMeanVarianceRelation()`
`String`	`getMetadata()`
`Integer`	`getNumberOfDataVectors()`
`Integer`	`getNumberOfSamples()`
`Set<ExpressionExperiment>`	`getOtherParts()`
`Set<ProcessedExpressionDataVector>`	`getProcessedExpressionDataVectors()`
`Set<QuantitationType>`	`getQuantitationTypes()`
`Set<RawExpressionDataVector>`	`getRawExpressionDataVectors()`
`String`	`getShortName()`
`String`	`getSource()`
`Taxon`	`getTaxon()` This is a denormalization to speed up queries.
`int`	`hashCode()` Returns a hash code based on this entity's identifiers.
`void`	`setBatchConfound(String batchConfound)`
`void`	`setBatchEffect(String batchEffect)`
`void`	`setBioAssays(Set<BioAssay> bioAssays)`
`void`	`setCurationDetails(CurationDetails curationDetails)`
`void`	`setExperimentalDesign(ExperimentalDesign experimentalDesign)`
`void`	`setGeeq(Geeq geeq)`
`void`	`setMeanVarianceRelation(MeanVarianceRelation meanVarianceRelation)`
`void`	`setMetadata(String metadata)`
`void`	`setNumberOfDataVectors(Integer numberOfDataVectors)`
`void`	`setNumberOfSamples(Integer numberofSamples)`
`void`	`setOtherParts(Set<ExpressionExperiment> otherParts)`
`void`	`setProcessedExpressionDataVectors(Set<ProcessedExpressionDataVector> processedExpressionDataVectors)`
`void`	`setQuantitationTypes(Set<QuantitationType> quantitationTypes)`
`void`	`setRawExpressionDataVectors(Set<RawExpressionDataVector> rawExpressionDataVectors)`
`void`	`setShortName(String shortName)`
`void`	`setSource(String source)`
`void`	`setTaxon(Taxon taxon)`
`String`	`toString()`

Methods inherited from class ubic.gemma.model.expression.experiment.BioAssaySet
getAccession, getBioAssays, setAccession

Methods inherited from class ubic.gemma.model.analysis.Investigation
getCharacteristics, getOtherRelevantPublications, getOwner, getPrimaryPublication, setCharacteristics, setOtherRelevantPublications, setOwner, setPrimaryPublication

Methods inherited from class ubic.gemma.model.common.AbstractAuditable
getAuditTrail, setAuditTrail

Methods inherited from class ubic.gemma.model.common.AbstractDescribable
getDescription, getId, getName, setDescription, setId, setName

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface gemma.gsec.model.Securable
getId

Methods inherited from interface ubic.gemma.model.common.Auditable
getAuditTrail, setAuditTrail

Methods inherited from interface ubic.gemma.model.common.Identifiable
getId

- 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)
```
  - createValueObject
```
public ExpressionExperimentValueObject createValueObject()
```
    Description copied from class: BioAssaySet
    
    Special use case. Use a constructor of the desired VO instead, or the loadValueObject() in all VO-Enabled services.
    
    Specified by:
    
    createValueObject in class BioAssaySet
    
    Returns:
    
    an expression experiment value object.
  - 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
  - getBatchConfound
```
public String getBatchConfound()
```
  - getBatchEffect
```
public String getBatchEffect()
```
  - getCurationDetails
```
public CurationDetails getCurationDetails()
```
    Specified by:
    
    getCurationDetails in interface Curatable
  - getExperimentalDesign
```
public ExperimentalDesign getExperimentalDesign()
```
  - getGeeq
```
public Geeq getGeeq()
```
  - getMeanVarianceRelation
```
public MeanVarianceRelation getMeanVarianceRelation()
```
  - getMetadata
```
public String getMetadata()
```
  - getNumberOfDataVectors
```
public Integer getNumberOfDataVectors()
```
    Returns:
    
    The number of ProcessedExpressionDataVectors associated with this.
  - getOtherParts
```
public Set<ExpressionExperiment> getOtherParts()
```
  - getProcessedExpressionDataVectors
```
public Set<ProcessedExpressionDataVector> getProcessedExpressionDataVectors()
```
  - getQuantitationTypes
```
public Set<QuantitationType> getQuantitationTypes()
```
  - getRawExpressionDataVectors
```
public Set<RawExpressionDataVector> getRawExpressionDataVectors()
```
  - getShortName
```
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)
  - hashCode
```
public int hashCode()
```
    Description copied from class: AbstractDescribable
    
    Returns a hash code based on this entity's identifiers.
    
    Overrides:
    
    hashCode in class AbstractDescribable
  - setBatchConfound
```
public void setBatchConfound(String batchConfound)
```
  - setBatchEffect
```
public void setBatchEffect(String batchEffect)
```
  - setBioAssays
```
public void setBioAssays(Set<BioAssay> bioAssays)
```
    Overrides:
    
    setBioAssays in class BioAssaySet
  - setCurationDetails
```
public void setCurationDetails(CurationDetails curationDetails)
```
    Specified by:
    
    setCurationDetails in interface Curatable
  - 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)
```
  - setOtherParts
```
public void setOtherParts(Set<ExpressionExperiment> otherParts)
```
  - setProcessedExpressionDataVectors
```
public void setProcessedExpressionDataVectors(Set<ProcessedExpressionDataVector> processedExpressionDataVectors)
```
  - 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)
```
  - 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)
```
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class AbstractDescribable
    
    See Also:
    
    AbstractDescribable.toString()

Class ExpressionExperiment

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class ubic.gemma.model.expression.experiment.BioAssaySet

Methods inherited from class ubic.gemma.model.analysis.Investigation

Methods inherited from class ubic.gemma.model.common.AbstractAuditable

Methods inherited from class ubic.gemma.model.common.AbstractDescribable

Methods inherited from class java.lang.Object

Methods inherited from interface gemma.gsec.model.Securable

Methods inherited from interface ubic.gemma.model.common.Auditable

Methods inherited from interface ubic.gemma.model.common.Identifiable

Constructor Detail

ExpressionExperiment

Method Detail

getNumberOfSamples

setNumberOfSamples

createValueObject

equals

getBatchConfound

getBatchEffect

getCurationDetails

getExperimentalDesign

getGeeq

getMeanVarianceRelation

getMetadata

getNumberOfDataVectors

getOtherParts

getProcessedExpressionDataVectors

getQuantitationTypes

getRawExpressionDataVectors

getShortName

getSource

hashCode

setBatchConfound

setBatchEffect

setBioAssays

setCurationDetails

setExperimentalDesign

setGeeq

setMeanVarianceRelation

setMetadata

setNumberOfDataVectors

setOtherParts

setProcessedExpressionDataVectors

setQuantitationTypes

setRawExpressionDataVectors

setShortName

setSource

getTaxon

setTaxon

toString