Working with MIAME Objects :: Microarray Analysis (Bioinformatics Toolbox™)

Working with MIAME Objects

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Overview of MIAME Objects Constructing MIAME Objects Using Properties and Methods of a MIAME Object

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Using Properties and Methods of a MIAME Object

Overview of MIAME Objects

A MIAME object contains 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
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

Import the bioma.data package so that the MIAME constructor function is available.
```
import bioma.data.*
```
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]
```
Use the MIAME constructor function to create a MIAME object from the structure.
```
MIAMEObj1 = MIAME(geoStruct);
```

Display information about the MIAME object, MIAMEObj.

MIAMEObj1 

Experiment Description:
  Author name: Mika,,Silvennoinen
Riikka,,KivelÃ¤
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 Using Properties

Import the bioma.data package so that theMIAME constructor function is available.
```
import bioma.data.*
```

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.'});

Display information about the MIAME object, 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.'