Representing All Data in an ExpressionSet Object

Overview of ExpressionSet Objects

You can store all microarray experiment data and information in one object by assembling the following into an ExpressionSet object:

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.

Constructing ExpressionSet Objects

Note

The following procedure assumes you have executed the example code in the previous sections:

Import the bioma package so that the ExpressionSet constructor function is available.
```
import bioma.*
```
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);
```

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.

Using Properties 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

Property names are case sensitive. For a list and description of all properties of an ExpressionSet object, see ExpressionSet class.

Using Methods of an ExpressionSet Object

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

objectname.methodname

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,,KivelÃ¤
Maarit,,Lehti
Anna-Maria,,Touvras
Jyrki,,Komulainen
Veikko,,Vihko
Heikki,,Kainulainen
  Laboratory: XYZ Lab
  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.