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Representing Expression Data Values in ExptData Objects

Overview of ExptData Objects

You can use an ExptData object to store expression values from a microarray experiment. An ExprData object stores the data values in one or more DataMatrix objects, each having the same row names (feature names) and column names (sample names). Each element (DataMatrix object) in the ExptData object has an element name.

The following illustrates a small DataMatrix object containing expression values from three samples (columns) and seven features (rows):

                  A         B         C     
    100001_at      2.26     20.14     31.66
    100002_at    158.86    236.25    206.27
    100003_at     68.11    105.45     82.92
    100004_at     74.32     96.68     84.87
    100005_at     75.05     53.17     57.94
    100006_at     80.36     42.89     77.21
    100007_at    216.64    191.32    219.48

An ExptData object lets you store, manage, and subset the data values from a microarray experiment. An ExptData object includes properties and methods that let you access, retrieve, and change data values from a microarray experiment. These properties and methods are useful to view and analyze the data. For a list of the properties and methods, see ExptData class.

Constructing ExptData Objects

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

  1. Import the bioma.data package so that the DataMatrix and ExptData constructor functions are available.

    import bioma.data.*
    
  2. Use the DataMatrix constructor function to create a DataMatrix object from the gene expression data in the mouseExprsData.txt file. This file contains a table of expression values and metadata (sample and feature names) from a microarray experiment done using the Affymetrix® MGU74Av2 GeneChip® array. There are 26 sample names (A through Z), and 500 feature names (probe set names).

    dmObj = DataMatrix('File', 'mouseExprsData.txt');
  3. Use the ExptData constructor function to create an ExptData object from the DataMatrix object.

    EDObj = ExptData(dmObj);
  4. Display information about the ExptData object, EDObj.

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

    Note:   For complete information on constructing ExptData objects, see ExptData class.

Using Properties of an ExptData Object

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

objectname.propertyname

For example, to determine the number of elements (DataMatrix objects) in an ExptData object:

EDObj.NElements

ans =

     1

To set properties of an ExptData object, use the following syntax:

objectname.propertyname = propertyvalue

For example, to set the Name property of an ExptData object:

EDObj.Name = 'MyExptDataObject'

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

Using Methods of an ExptData Object

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

objectname.methodname

or

methodname(objectname)

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

EDObj.sampleNames

Columns 1 through 9

    'A'    'B'    'C'    'D'    'E'    'F'    'G'    'H'    'I'  ...

To return the size of an ExptData object:

size(EDObj)

ans =

   500    26

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

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.

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