bioma.ExpressionSet class - Package: bioma
Superclasses: bioma.AExperiment

Contain data from microarray gene expression experiment

Description

The ExpressionSet class is designed to contain data from a microarray gene expression experiment, including expression values, sample and feature metadata, and information about experimental methods and conditions. It provides a convenient way to store related information about a microarray gene expression experiment in a single data structure (object). It also lets you manage and subset the data.

The ExpressionSet class includes properties and methods that let you access, retrieve, and change data, metadata, and other information about the microarray gene expression experiment. These properties and methods are useful for viewing and analyzing the data.

Construction

ExprSetobj = bioma.ExpressionSet(Data) creates an ExpressionSet object, from Data, a numeric matrix, a DataMatrix object, or an ExptData object, which contains one or more DataMatrix objects with the same dimensions, row names and column names.

ExprSetobj = bioma.ExpressionSet(Data, {DMobj1, Name1}, {DMobj2, Name2}, ...) creates an ExpressionSet object, from Data, and additional DataMatrix objects with specified element names. All DataMatrix objects must have the same dimensions, row names, and column names.

ExprSetobj = bioma.ExpressionSet(..., 'PropertyName', PropertyValue) constructs the object using options, specified as property name/property value pairs.

ExprSetobj = bioma.ExpressionSet(..., 'SData', SDataValue) includes a MetaData object containing sample metadata in the ExpressionSet object.

ExprSetobj = bioma.ExpressionSet(..., 'FData', FDataValue) includes a MetaData object containing microarray feature metadata in the ExpressionSet object.

ExprSetobj = bioma.ExpressionSet(..., 'EInfo', EInfoValue) includes a MIAME object, which contains experiment information, in the ExpressionSet object.

Input Arguments

Data

Any of the following: Numeric matrix DataMatrix object ExptData object, which contains one or more DataMatrix objects having the same dimensions If you provide a DataMatrix object, bioma.ExpressionSet creates an ExptData object from it and names the DataMatrix object Expressions. If you provide an ExptData object, bioma.ExpressionSet renames the first DataMatrix object in the ExptData object to Expressions, unless another DataMatrix object in the ExptData object is already named Expressions.

DMobj#

Variable name of a DataMatrix object. Each DataMatrix object must have the same dimensions as Data.

Name#

String specifying an element name for the corresponding DataMatrix object. Each DataMatrix object in an ExpressionSet object has an element name. At least one DataMatrix object in an ExpressionSet object has an element name of Expressions. By default, it is the first DataMatrix object.

SDataValue

Variable name of a MetaData object containing sample metadata for the experiment. The variable name must exist in the MATLAB Workspace.

FDataValue

Variable name of a MetaData object containing microarray feature metadata for the experiment. The variable name must exist in the MATLAB Workspace.

EInfoValue

Variable name of a MIAME object, which contains information about the experiment methods and conditions. The variable name must exist in the MATLAB Workspace.

Properties

NElements	Number of elements in the experiment Positive integer specifying the number of elements (DataMatrix objects) in the experiment data. This value is equivalent to the number of DataMatrix objects in the ExperimentSet object. This information is read-only. Attributes: SetAccess private
NFeatures	Number of features in the experiment Positive integer specifying the number of features in the experiment. This value is equivalent to the number of rows in each DataMatrix object in the ExperimentSet object. This information is read-only. Attributes: SetAccess private
NSamples	Number of samples in the experiment Positive integer specifying the number of samples in the experiment. This value is equivalent to the number of columns in each DataMatrix object in the ExperimentSet object. This information is read-only. Attributes: SetAccess private

Methods

abstract	Retrieve or set abstract describing experiment in ExpressionSet object
elementData	Retrieve or set data element (DataMatrix object) in ExpressionSet object
elementNames	Retrieve or set element names of DataMatrix objects in ExpressionSet object
expressions	Retrieve or set Expressions DataMatrix object from ExpressionSet object
exprWrite	Write expression values in ExpressionSet object to text file
exptData	Retrieve or set experiment data in ExpressionSet object
exptInfo	Retrieve or set experiment information in ExpressionSet object
featureData	Retrieve or set feature metadata in ExpressionSet object
featureNames	Retrieve or set feature names in ExpressionSet object
featureVarDesc	Retrieve or set feature variable descriptions in ExpressionSet object
featureVarNames	Retrieve or set feature variable names in ExpressionSet object
featureVarValues	Retrieve or set feature variable data values in ExpressionSet object
pubMedID	Retrieve or set PubMed IDs in ExpressionSet object
sampleData	Retrieve or set sample metadata in ExpressionSet object
sampleNames	Retrieve or set sample names in ExpressionSet object
sampleVarDesc	Retrieve or set sample variable descriptions in ExpressionSet object
sampleVarNames	Retrieve or set sample variable names in ExpressionSet object
sampleVarValues	Retrieve or set sample variable values in ExpressionSet object
size	Return size of ExpressionSet object

Instance Hierarchy

An ExpressionSet object contains an ExptData object, two MetaData objects, and a MIAME object. These objects can be empty.

Attributes

To learn about attributes of classes, see Class Attributes in the MATLAB Object-Oriented Programming documentation.

Copy Semantics

Value. To learn how this affects your use of the class, see Copying Objects in the MATLAB Programming Fundamentals documentation.

Indexing

ExpressionSet objects support 2-D parenthesis ( ) indexing to extract, assign, and delete data.

ExpressionSet objects do not support:

• Dot . indexing

• Curly brace { } indexing

• Linear indexing

Examples

The mouseExprsData.txt file used in this example contains data from Hovatta et al., 2005.

Construct an ExpressionSet object from EDObj, an ExptData object; MDObj2, a MetaData object containing sample variable information; and MIAMEObj, a MIAME object:

% Import bioma.data package to make constructor functions
% available
import bioma.data.*
% Create DataMatrix object from .txt file containing 
% expression values from microarray experiment
dmObj = DataMatrix('File', 'mouseExprsData.txt');
% Construct ExptData object
EDObj = ExptData(dmObj);
% Construct MetaData object from .txt file
MDObj2 = MetaData('File', 'mouseSampleData.txt', 'VarDescChar', '#');
% Create a MATLAB structure containing GEO Series data
geoStruct = getgeodata('GSE4616');
% Construct MIAME object
MIAMEObj = MIAME(geoStruct);
% Import bioma package to make constructor function
% available
import bioma.*
% Construct ExpressionSet object
ESObj = ExpressionSet(EDObj, 'SData', MDObj2, 'EInfo', MIAMEObj);
% Display information about the ExpressionSet object
ESObj

References

[1] Hovatta, I., Tennant, R S., Helton, R., et al. (2005). Glyoxalase 1 and glutathione reductase 1 regulate anxiety in mice. Nature 438, 662–666.

See Also

bioma.data.ExptData | bioma.data.MetaData | bioma.data.MIAME

Tutorials

• Working with Objects for Microarray Experiment Data
• Analyzing Illumina Bead Summary Gene Expression Data

How To

• Class Attributes
• Property Attributes
• Storing and Managing Gene Expression Data in Objects

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