bioma.ExpressionSet Class

Namespace: bioma
Superclasses:

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#

Character vector or 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
exprWrite	Write expression values in ExpressionSet object to text file
expressions	Retrieve or set Expressions DataMatrix object from ExpressionSet object
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.

Copy Semantics

Value. To learn how this affects your use of the class, see Copying Objects.

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

Construct an ExpressionSet Object

This example shows how to construct an ExpressionSet object. The mouseExprsData.txt file used in this example contains data from Hovatta et al., 2005.

Import the bioma.data namespace to make the constructor function available.

import bioma.data.*

Create a DataMatrix object from .txt file containing expression values from microarray experiment.

dmObj = DataMatrix('File', 'mouseExprsData.txt');

Construct an ExptData object.

EDObj = ExptData(dmObj)

EDObj = 

Experiment Data:
  500 features,  26 samples
  1 elements
  Element names: Elmt1

Construct a MetaData object from .txt file.

MDObj2 = MetaData('File', 'mouseSampleData.txt', 'VarDescChar', '#')

MDObj2 = 

Sample Names:
    A, B, ...,Z (26 total)
Variable Names and Meta Information:
              VariableDescription                         
    Gender    ' Gender of the mouse in study'             
    Age       ' The number of weeks since mouse birth'    
    Type      ' Genetic characters'                       
    Strain    ' The mouse strain'                         
    Source    ' The tissue source for RNA collection' 

Create a MATLAB structure containing GEO Series data.

geoStruct = getgeodata('GSE4616');

Construct a MIAME object.

MIAMEObj = MIAME(geoStruct)

MIAMEObj = 

Experiment Description:
  Author name: Mika,,Silvennoinen
Riikka,,Kivelä
Maarit,,Lehti
Anna-Maria,,Touvras
Jyrki,,Komulainen
Veikko,,Vihko
Heikki,,Kainulainen
  Laboratory: LIKES - Research Center
  Contact information: Mika,,Silvennoinen
  URL: 
  PubMedIDs: 17003243
  Abstract: A 90 word abstract is available. Use the Abstract property.
  Experiment Design: A 234 word summary is available. Use the ExptDesign property.
  Other notes: 
    [1x84 char]

Import the bioma namespace to make constructor function available.

import bioma.*

Construct an ExpressionSet object.

ESObj = ExpressionSet(EDObj, 'SData', MDObj2, 'EInfo', MIAMEObj)

ESObj = 

ExpressionSet
Experiment Data: 500 features, 26 samples
  Element names: Expressions
Sample Data:
    Sample names:     A, B, ...,Z (26 total)
    Sample variable names and meta information: 
        Gender:  Gender of the mouse in study
        Age:  The number of weeks since mouse birth
        Type:  Genetic characters
        Strain:  The mouse strain
        Source:  The tissue source for RNA collection
Feature Data: none
Experiment Information: use 'exptInfo(obj)'

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.