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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

combineCombine two MIAME objects
isemptyDetermine 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

expand all

Construct a MIAME object

Create a MATLAB structure containing Gene Expression Omnibus (GEO) series data.

geoStruct = getgeodata('GSE4616');

Import bioma.data package to make the constructor function available.

import bioma.data.*

Construct MIAME object from the structure.

MIAMEObj1 = MIAME(geoStruct)
MIAMEObj1 = 

Experiment Description:
  Author name: Mika,,Silvennoinen
Riikka,,Kivelä
Maarit,,Lehti
Anna-Maria,,Touvras
Jyrki,,Komulainen
Veikko,,Vihko
Heikki,,Kainulainen
  Laboratory: LIKES - Research Center
  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: 
    [1x84 char]

Supply a URL for the MIAME object.

MIAMEObj1.URL = 'www.nonexistinglab.com'
MIAMEObj1 = 

Experiment Description:
  Author name: Mika,,Silvennoinen
Riikka,,Kivelä
Maarit,,Lehti
Anna-Maria,,Touvras
Jyrki,,Komulainen
Veikko,,Vihko
Heikki,,Kainulainen
  Laboratory: LIKES - Research Center
  Contact information: Mika,,Silvennoinen
  URL: www.nonexistinglab.com
  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: 
    [1x84 char]

Alternatively you can construct a MIAME object using customized properties.

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.'})
MIAMEObj2 = 

Experiment Description:
  Author name: Jane Researcher
  Laboratory: One Bioinformatics Laboratory
  Contact information: jresearcher@lab.not.exist
  URL: www.lab.not.exist
  PubMedIDs: 
  Abstract: A 4 word abstract is available. Use the Abstract property.
  No experiment design summary available.
  Other notes: 
    'Notes:Created from a text file.'

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