bioma.data.MIAME

Contain experiment information from microarray gene expression experiment

expand all in page

Description

The bioma.data.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 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 bioma.data.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.

Creation

Syntax

MIAMEobj = bioma.data.MIAME()
MIAMEobj = bioma.data.MIAME(GeoSeriesStruct)
MIAMEobj = bioma.data.MIAME(___,Name,Value)

Description

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.

example

MIAMEobj = bioma.data.MIAME(___,Name,Value) sets the object properties using one or more name-value pair arguments. Enclose each property name in quotes. For example, MIAMEobj = bioma.data.MIAME('Other','Cannabinoid Receptor 2') sets the value of the property Other to Cannabinoid Receptor 2.

example

Input Arguments

expand all

Gene Expression Omnibus (GEO) Series data, specified as a structure. You can generate the structure using one of the following:

  • getgeodata

  • Structure.Header.Series substructure returned by getgeodata

Output Arguments

expand all

MIAME object, returned as a bioma.ma.MIAME object.

Properties

expand all

Name of the experiment investigator, specified as a character vector.

Name of the laboratory where the experiment was conducted, specified as a character vector.

Contact information for the experiment investigator or laboratory, specified as a character vector

Character array containing contact information for the experiment investigator or laboratory.

URL for the experiment, specified as a character vector.

Title for the experiment, specified as a character vector.

Abstract describing the experiment, specified as a character vector.

Description of the experiment design, specified as a character vector.

Information about the microarray chips used in the experiment, specified as a character vector or cell array of character vectors.

Information can include array name, array platform, number of features on the array, and so on.

Information about samples used in the experiment, specified as a character vector or cell array of character vectors.

Information can include sample source, sample organism, treatment type, compound, labeling protocol, external control, and so on.

Information about the experiment hybridization, specified as a character vector or cell array of character vectors.

Information can include hybridization time, concentration, volume, temperature, and so on.

Information about the experiment quality controls, specified as a character vector or cell array of character vectors.

Information can include replicates, dye swap, and so on.

Information about the preprocessing steps used on the experimental data, specified as a character vector or cell array of character vectors.

PubMed identifiers for relevant publications, specified as a character vector.

Other information about the experiment not covered by other properties, specified as a character vector or cell array of character vectors.

Object Functions

combineCombine two MIAME objects
isemptyDetermine whether MIAME object is empty

Examples

collapse all

Open Live Script

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

geoStruct = getgeodata('GSE292193');

Construct a MIAME object from the structure. 

miameObj1 = bioma.data.MIAME(geoStruct)
miameObj1 = 
Experiment Description:
  Author name: Yukun,,GUAN
Yang,,WANG
Bin,,GAO
  Laboratory: NIAAA
  Contact information: Yukun,,Guan
  URL: 
  PubMedIDs: 
  Abstract: A 97 word abstract is available. Use the Abstract property.
  Experiment Design: A 114 word summary is available. Use the ExptDesign property.
  Other notes: 
    {'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE292nnn/GSE292193/suppl/GSE292193_EtOH_ApoE_vs_EtOH_WT.txt.gz'}

Add a URL for the object.

miameObj1.URL = 'www.nih.gov'
miameObj1 = 
Experiment Description:
  Author name: Yukun,,GUAN
Yang,,WANG
Bin,,GAO
  Laboratory: NIAAA
  Contact information: Yukun,,Guan
  URL: www.nih.gov
  PubMedIDs: 
  Abstract: A 97 word abstract is available. Use the Abstract property.
  Experiment Design: A 114 word summary is available. Use the ExptDesign property.
  Other notes: 
    {'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE292nnn/GSE292193/suppl/GSE292193_EtOH_ApoE_vs_EtOH_WT.txt.gz'}


MIAMEObj2 = bioma.data.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.'}

Version History

Introduced in R2009b