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Working with ExpressionSet Objects

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Overview of ExpressionSet Objects Constructing ExpressionSet Objects Using Properties and Methods of an ExpressionSet Object

Overview of ExpressionSet Objects

An ExpressionSet object contains information from a microarray gene expression experiment. The information from such an experiment is typically subdivided into four categories:

• Measured expression values

• Sample metadata

• Microarray feature metadata

• Descriptions of experiment methods and conditions

An ExpressionSet object typically contains the previous information in:

• One ExptData object containing expression values from a microarray experiment in one or more DataMatrix objects

• One MetaData object containing sample metadata in two dataset arrays

• One MetaData object containing feature metadata in two dataset arrays

• One MIAME object containing experiment descriptions

The following graphic illustrates a typical ExpressionSet object and its component objects.

Each element (DataMatrix object) in the ExpressionSet object has an element name. Also, there is always one DataMatrix object whose element name is Expressions.

An ExpressionSet object lets you store, manage, and subset the data from a microarray gene expression experiment. An ExpressionSet object includes properties and methods that let you access, retrieve, and change data, metadata, and other information about the microarray experiment. These properties and methods are useful to view and analyze the data. For a list of the properties and methods, see ExpressionSet class.

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Constructing ExpressionSet Objects

1. Import the bioma package so that the ExpresssionSet constructor function is available.

   import bioma.*
   

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

   ESObj = ExpressionSet(EDObj, 'SData', MDObj2, 'EInfo', MIAMEObj1);
   

3. Display information about the ExpressionSet object, ESObj.

   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)'

For complete information on constructing ExpressionSet objects, see ExpressionSet class.

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Using Properties and Methods of an ExpressionSet Object

To access properties of an ExpressionSet object, use the following syntax:

objectname.propertyname

For example, to determine the number of samples in an ExpressionSet object:

ESObj.NSamples

ans =

    26

Note   For a list and description of all properties of an ExpressionSet object, see ExpressionSet class.

To use methods of an ExpressionSet object, use either of the following syntaxes:

objectname.methodname

or

methodname(objectname)

For example, to retrieve the sample variable names from an ExpressionSet object:

ESObj.sampleVarNames

ans = 

    'Gender'    'Age'    'Type'    'Strain'    'Source'

To retrieve the experiment information contained in an ExpressionSet object:

exptInfo(ESObj)

ans = 

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: 
    [1x80 char]

Note   For a complete list of methods of an ExpressionSet object, see ExpressionSet class.

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Microarray Analysis

Working with ExptData Objects

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