bioma.data.MIAME class - Package: bioma.data

Contain experiment information from microarray gene expression experiment

Description

The MIAME class is designed to contain information about experimental methods and conditions from a microarray gene expression experiment. It loosely follows the Minimum Information About a Microarray Experiment (MIAME) specification. It can include information about:

Experiment design
Microarrays used in the experiment
Samples used
Sample preparation and labeling
Hybridization procedures and parameters
Normalization controls
Preprocessing information
Data processing specifications

It provides a convenient way to store related information about a microarray experiment in a single data structure (object).

The MIAME class includes properties and methods that let you access, retrieve, and change experiment information related to a microarray experiment. These properties and methods are useful to view and analyze the information.

Construction

MIAMEobj = bioma.data.MIAME() creates an empty MIAME object for storing experiment information from a microarray gene expression experiment.

MIAMEobj = bioma.data.MIAME(GeoSeriesStruct) creates a MIAME object from a structure containing Gene Expression Omnibus (GEO) Series data.

MIAMEobj = bioma.data.MIAME(..., 'PropertyName', PropertyValue) constructs the object using options, specified as property name/property value pairs.

MIAMEobj = bioma.data.MIAME(...,'Investigator', InvestigatorValue) specifies the name of the experiment investigator.

MIAMEobj = bioma.data.MIAME(...,'Lab', LabValue) specifies the laboratory that conducted the experiment.

MIAMEobj = bioma.data.MIAME(...,'Contact', ContactValue) specifies the contact information for the experiment investigator or laboratory.

MIAMEobj = bioma.data.MIAME(...,'URL', URLValue) specifies the experiment URL.

Inputs

`GeoSeriesStruct`	Gene Expression Omnibus (GEO) Series data specified by either: MATLAB structure returned by the `getgeodata` function `Structure.Header.Series` substructure returned by the `getgeodata` function
`InvestigatorValue`	String specifying the name of the experiment investigator.
`LabValue`	String specifying the laboratory that conducted the experiment.
`ContactValue`	String specifying the contact information for the experiment investigator or laboratory
`URLValue`	String specifying the experiment URL.

Properties

`Abstract`	Abstract describing the experiment String containing an abstract describing the experiment.
`Arrays`	Information about the microarray chips used in the experiment Cell array containing information about the microarray chips used in the experiment. Information can include array name, array platform, number of features on the array, and so on.
`Contact`	Contact information for the experiment investigator or laboratory Character array containing contact information for the experiment investigator or laboratory.
`ExptDesign`	Brief description of the experiment design Character array containing description of the experiment design.
`Hybridization`	Information about the experiment hybridization Cell array containing information about the hybridization protocol used in the experiment. Information can include hybridization time, concentration, volume, temperature, and so on.
`Investigator`	Name of the experiment investigator Character array containing the name of the experiment investigator.
`Laboratory`	Name of the laboratory where the experiment was conducted Character array containing the name of laboratory.
`Other`	Other information about the experiment Cell array containing other information about the experiment, not covered by the other properties.
`Preprocessing`	Information about the experiment preprocessing steps Cell array containing information about the preprocessing steps used on the data from the experiment.
`PubMedID`	PubMed identifiers for relevant publications. Character array containing PubMed identifiers for papers relevant to the data set used in the experiment.
`QualityControl`	Information about the experiment quality controls Cell array containing information about the experiment quality control steps. Information can include replicates, dye swap, and so on.
`Samples`	Information about samples used in the experiment Cell array containing information about the samples used in the experiment. Information can include sample source, sample organism, treatment type, compound, labeling protocol, external control, and so on.
`Title`	Experiment title Character array containing a single sentence experiment title.
`URL`	URL for the experiment Character array containing URL for the experiment.

Methods

combine	Combine two MIAME objects
isempty	Determine whether MIAME object is empty

Instance Hierarchy

An ExpressionSet object contains a MIAME object.

Attributes

To learn about attributes of classes, see Class Attributes in the MATLAB Object-Oriented Programming documentation.

Copy Semantics

Value. To learn how this affects your use of the class, see Copying Objects in the MATLAB Programming Fundamentals documentation.

Examples

Construct a MIAME object from a structure containing information from a Gene Expression Omnibus (GEO) Series record:

% Create a MATLAB structure containing GEO Series data
geoStruct = getgeodata('GSE4616');
% Import bioma.data package to make constructor function
% available
import bioma.data.*
% Construct MIAME object
MIAMEObj1 = MIAME(geoStruct);
% Display information about the MIAME object
MIAMEObj1
% Supply a URL for the MIAME object
MIAMEObj1.URL = 'www.nonexistinglab.com'

Construct a MIAME object using properties:

% Import bioma.data package to make constructor function
% available
import bioma.data.*
% Construct MIAME object
MIAMEObj2 = MIAME('investigator', 'Jane Researcher',...
                  'lab', 'One Bioinformatics Laboratory',...
                  'contact', 'jresearcher@lab.not.exist',...
                  'url', 'www.lab.not.exist',...
                  'title', 'Normal vs. Diseased Experiment',...
                  'abstract', 'Example of using expression data',...
                  'other', {'Notes:Created from a text file.'});
% Display information about the MIAME object
MIAMEObj2
% Replace the URL for the MIAME object
MIAMEObj2.URL = 'www.nonexistinglab.com'