Documentation

Representing Experiment Information in a MIAME Object

Overview of MIAME Objects

You can store information about experimental methods and conditions from a microarray gene expression experiment in a MIAME object. It loosely follows the Minimum Information About a Microarray Experiment (MIAME) specification. It can include information about:

  • Experiment design

  • Microarrays used

  • Samples used

  • Sample preparation and labeling

  • Hybridization procedures and parameters

  • Normalization controls

  • Preprocessing information

  • Data processing specifications

A MIAME object 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. For a list of the properties and methods, see MIAME class.

Constructing MIAME Objects

For complete information on constructing MIAME objects, see MIAME class.

Constructing a MIAME Object from a GEO Structure

  1. Import the bioma.data package so that the MIAME constructor function is available.

    import bioma.data.*
    
  2. Use the getgeodata function to return a MATLAB® structure containing Gene Expression Omnibus (GEO) Series data related to accession number GSE4616.

    geoStruct = getgeodata('GSE4616')
    
    geoStruct = 
    
        Header: [1x1 struct]
          Data: [12488x12 bioma.data.DataMatrix]
  3. Use the MIAME constructor function to create a MIAME object from the structure.

    MIAMEObj1 = MIAME(geoStruct);
  4. Display information about the MIAME object, MIAMEObj.

    MIAMEObj1 
    
    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: 
        [1x80 char]

Constructing a MIAME Object from Properties

  1. Import the bioma.data package so that theMIAME constructor function is available.

    import bioma.data.*
    
  2. Use the MIAME constructor function to create a MIAME object using individual 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.'});
  3. Display information about the MIAME object, MIAMEObj2.

    MIAMEObj2
    
    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.'

Using Properties of a MIAME Object

To access properties of a MIAME object, use the following syntax:

objectname.propertyname

For example, to retrieve the PubMed identifier of publications related to a MIAME object:

MIAMEObj1.PubMedID

ans =

17003243

To set properties of a MIAME object, use the following syntax:

objectname.propertyname = propertyvalue

For example, to set the Laboratory property of a MIAME object:

MIAMEObj1.Laboratory = 'XYZ Lab'

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

Using Methods of a MIAME Object

To use methods of a MIAME object, use either of the following syntaxes:

objectname.methodname

or

methodname(objectname)

For example, to determine if a MIAME object is empty:

MIAMEObj1.isempty

ans =

     0

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

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