MIAME                package:Biobase                R Documentation

Class for Storing Microarray Experiment Information

Description:

     Class 'MIAME' covers MIAME entries that are not covered by other
     classes in Bioconductor. Namely, experimental design, samples,
     hybridizations, normalization controls, and pre-processing
     information.

Slots:


     'name': Object of class 'character' containing the experimenter
          name

     'lab': Object of class 'character' containing the laboratory where
          the experiment was conducted

     'contact': Object of class 'character' containing contact
          information for lab and/or experimenter

     'title': Object of class 'character' containing a single-sentence
          experiment title 

     'abstract': Object of class 'character' containing an abstract
          describing the experiment

     'url': Object of class 'character' containing a URL for the
          experiment

     'samples': Object of class 'list' containing information about the
          samples

     'hybridizations': Object of class 'list' containing information
          about the hybridizations

     'normControls': Object of class 'list' containing information
          about the controls such as house keeping genes

     'preprocessing': Object of class 'list' containing information
          about the pre-processing steps used on the raw data from this
          experiment

     'pubMedIds': Object of class 'character' listing strings of PubMed
          identifiers of papers relevant to the dataset

     'other': Object of class 'list' containing other information for
          which none of the above slots does not applies

Methods:

     Class-specific methods:

     'abstract(MIAME)': An accessor function for 'abstract'.

     'combine(MIAME,MIAME)': Combine two objects of 'MIAME-class',
          issuing warnings when ambiguities encountered.

     'expinfo(MIAME)': An accessor function for 'name', 'lab',
          'contact', 'title', and 'url'.

     'hybridizations(MIAME)': An accessor function for
          'hybridizations'.

     'normControls(MIAME)': An accessor function for 'normControls'.

     'notes(MIAME), notes(MIAME) <- value': Accessor functions for
          'other'. 'notes(MIAME) <- character' _appends_ character to
          notes; use 'notes(MIAME) <- list' to replace the notes
          entirely.

     'otherInfo(MIAME)': An accessor function for 'other'.

     'preproc(MIAME)': An accessor function for 'preprocessing'.

     'pubMedIds(MIAME), pubMedIds(MIAME) <- value': Accessor function
          for 'pubMedIds'.

     'samples(MIAME)': An accessor function for 'samples'.

     Standard generic methods:

     'updateObject(object, ..., verbose=FALSE)' Update instance to
          current version, if necessary. See 'updateObject'

     'isCurrent(object)' Determine whether version of object is
          current. See 'isCurrent'

     'isVersioned(object)' Determine whether object contains a
          'version' string describing its structure . See 'isVersioned'

     'show(MIAME)': Renders information about the MIAME information 

Author(s):

     Rafael A. Irizarry

References:

     <URL: http://www.mged.org/Workgroups/MIAME/miame_1.1.html>

See Also:

     'class:characterORMIAME', 'read.MIAME'

