MIAME

Class for Storing Microarray Experiment Information

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. The MIAME class is derived from MIAxE.

Keywords
classes
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

Constructor methods:

MIAME():
MIAME(name = "", lab = "", contact = "", title = "", abstract = "", url = "", pubMedIds = "" , samples = "", hybridizations = list(), normControls = list(), preprocessing = list(), other = list()): Creates a new MIAME object with slots as defined above.
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

References

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

See Also

class:characterORMIAME, read.MIAME

Aliases
  • class:MIAME
  • MIAME
  • MIAME-class
  • abstract,MIAME-method
  • combine,MIAME,MIAME-method
  • expinfo,MIAME-method
  • hybridizations,MIAME-method
  • normControls,MIAME-method
  • otherInfo,MIAME-method
  • preproc
  • preproc,MIAME-method
  • preproc<-,MIAME-method
  • preproc<-
  • notes,MIAME-method
  • notes<-,MIAME,list-method
  • notes<-,MIAME,character-method
  • pubMedIds,MIAME-method
  • pubMedIds<-,MIAME,ANY-method
  • samples,MIAME-method
  • show,MIAME-method
  • updateObject,MIAME-method
  • isCurrent,MIAME,missing-method
  • samples
Documentation reproduced from package Biobase, version 2.26.0, License: Artistic-2.0

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