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.

Input Arguments

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'

See Also

bioma.data.ExptData | bioma.data.MetaData | bioma.ExpressionSet | getgeodata

Tutorials

• Working with Objects for Microarray Experiment Data
• Analyzing Illumina Bead Summary Gene Expression Data

How To

• Class Attributes
• Property Attributes
• Representing Experiment Information in a MIAME Object

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