MIAME:
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. The MIAME class
is derived from MIAxE.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