Package ubic.gemma.model.expression.bioAssayData

Class ProcessedExpressionDataVector

java.lang.Object

ubic.gemma.model.expression.bioAssayData.DataVector

ubic.gemma.model.expression.bioAssayData.DesignElementDataVector

ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector

All Implemented Interfaces:

Serializable, Identifiable

public class ProcessedExpressionDataVector
extends DesignElementDataVector

Represents the processed data that is used for actual analyses. The vectors in this class would have been masked to remove missing values.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	ProcessedExpressionDataVector.Factory

Constructor Summary

Constructors

Constructor	Description
ProcessedExpressionDataVector()

Method Summary

Modifier and Type	Method	Description
ExpressionExperiment	getExpressionExperiment()
Double	getRankByMax()
Double	getRankByMean()
void	setExpressionExperiment(ExpressionExperiment expressionExperiment)
void	setRankByMax(Double rankByMax)
void	setRankByMean(Double rankByMean)
String	toString()

Methods inherited from class ubic.gemma.model.expression.bioAssayData.DesignElementDataVector

getBioAssayDimension, getDesignElement, setBioAssayDimension, setDesignElement

Methods inherited from class ubic.gemma.model.expression.bioAssayData.DataVector

equals, getData, getId, getQuantitationType, hashCode, setData, setId, setQuantitationType

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

ProcessedExpressionDataVector

public ProcessedExpressionDataVector()

Method Detail

toString

public String toString()

Overrides:

toString in class Object

getExpressionExperiment

public ExpressionExperiment getExpressionExperiment()

Specified by:

getExpressionExperiment in class DesignElementDataVector

setExpressionExperiment

public void setExpressionExperiment(ExpressionExperiment expressionExperiment)

Specified by:

setExpressionExperiment in class DesignElementDataVector

getRankByMax

public Double getRankByMax()

Returns:

The relative expression level of this vector in the study. Used as a quick-and-dirty way to provide feedback about the expession level without referring to any absolute baseline other than the minimum in the entire dataset, based on the maximum expression measurement for the probe (so the probe with the lowest expression is the one with the lowest maximum value). For two-color data sets, this is computed using the intensity values for the probe in the two channels, not from the ratios stored in this vector. For one-color data sets, this is computed directly from the intensity levels in this vector.

setRankByMax

public void setRankByMax(Double rankByMax)

getRankByMean

public Double getRankByMean()

Returns:

The relative expression level of this vector in the study. Used as a quick-and-dirty way to provide feedback about the expession level without referring to any absolute baseline other than the minimum in the entire dataset, based on the mean expression measurement for the probe. For two-color data sets, this is computed using the intensity values for the probe in the two channels, not from the ratios stored in this vector. For one-color data sets, this is computed directly from the intensity levels in this vector.

setRankByMean

public void setRankByMean(Double rankByMean)