Learn more about Bioinformatics Toolbox

Working with ExptData Objects

On this page…
Overview of ExptData Objects Constructing ExptData Objects Using Properties and Methods of an ExptData Object References

Overview of ExptData Objects

An ExptData object contains data values from a microarray experiment. It 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.

Back to Top

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.

Back to Top

Using Properties and Methods 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

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

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.

Back to Top

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.

Back to Top

Working with ExpressionSet Objects

Working with MetaData Objects

© 1984-2009- The MathWorks, Inc.    -   Site Help   -   Patents   -   Trademarks   -   Privacy Policy   -   Preventing Piracy   -   RSS