You can store all microarray experiment data and information in one object by assembling the following into an ExpressionSet object:
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
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.
The following procedure assumes you have executed the example code in the previous sections:
bioma package so that the
constructor function is available.
Construct an ExpressionSet object from
an ExptData object,
MDObj2, a MetaData object containing
sample variable information, and
MIAMEObj, a MIAME
ESObj = ExpressionSet(EDObj, 'SData', MDObj2, 'EInfo', MIAMEObj1);
Display information about the ExpressionSet object,
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.
To access properties of an ExpressionSet object, use the following syntax:
For example, to determine the number of samples in an ExpressionSet object:
ESObj.NSamples ans = 26
Property names are case sensitive. 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:
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]
For a complete list of methods of an ExpressionSet object, see ExpressionSet class.