\HeaderA{MIAME}{Class for Storing Microarray Experiment Information}{MIAME}
\aliasA{abstract,MIAME-method}{MIAME}{abstract,MIAME.Rdash.method}
\aliasA{class:MIAME}{MIAME}{class:MIAME}
\aliasA{combine,MIAME,MIAME-method}{MIAME}{combine,MIAME,MIAME.Rdash.method}
\aliasA{expinfo,MIAME-method}{MIAME}{expinfo,MIAME.Rdash.method}
\aliasA{hybridizations,MIAME-method}{MIAME}{hybridizations,MIAME.Rdash.method}
\aliasA{isCurrent,MIAME,missing-method}{MIAME}{isCurrent,MIAME,missing.Rdash.method}
\aliasA{MIAME-class}{MIAME}{MIAME.Rdash.class}
\aliasA{normControls,MIAME-method}{MIAME}{normControls,MIAME.Rdash.method}
\aliasA{notes,MIAME-method}{MIAME}{notes,MIAME.Rdash.method}
\aliasA{notes<-,MIAME,character-method}{MIAME}{notes<.Rdash.,MIAME,character.Rdash.method}
\aliasA{notes<-,MIAME,list-method}{MIAME}{notes<.Rdash.,MIAME,list.Rdash.method}
\aliasA{otherInfo,MIAME-method}{MIAME}{otherInfo,MIAME.Rdash.method}
\aliasA{preproc}{MIAME}{preproc}
\aliasA{preproc,MIAME-method}{MIAME}{preproc,MIAME.Rdash.method}
\aliasA{preproc<\Rdash}{MIAME}{preproc<.Rdash.}
\aliasA{preproc<-,MIAME-method}{MIAME}{preproc<.Rdash.,MIAME.Rdash.method}
\aliasA{pubMedIds,MIAME-method}{MIAME}{pubMedIds,MIAME.Rdash.method}
\aliasA{pubMedIds<-,MIAME,ANY-method}{MIAME}{pubMedIds<.Rdash.,MIAME,ANY.Rdash.method}
\aliasA{samples}{MIAME}{samples}
\aliasA{samples,MIAME-method}{MIAME}{samples,MIAME.Rdash.method}
\aliasA{show,MIAME-method}{MIAME}{show,MIAME.Rdash.method}
\aliasA{updateObject,MIAME-method}{MIAME}{updateObject,MIAME.Rdash.method}
\keyword{classes}{MIAME}
\begin{Description}\relax
Class \code{MIAME} covers MIAME entries that are not covered by other classes in Bioconductor. Namely, experimental design, samples, hybridizations, normalization controls, and pre-processing information.
\end{Description}
\begin{Section}{Slots}
\describe{
\item[\code{name}:] Object of class \code{character} containing the experimenter name
\item[\code{lab}:] Object of class \code{character} containing the laboratory where the experiment was conducted
\item[\code{contact}:] Object of class \code{character} containing contact information for lab and/or experimenter
\item[\code{title}:] Object of class \code{character} containing a single-sentence experiment title 
\item[\code{abstract}:] Object of class \code{character} containing an abstract describing the experiment
\item[\code{url}:] Object of class \code{character} containing a URL for the experiment
\item[\code{samples}:] Object of class \code{list} containing information about the samples
\item[\code{hybridizations}:] Object of class \code{list} containing information about the hybridizations
\item[\code{normControls}:] Object of class \code{list} containing information about the controls such as house keeping genes
\item[\code{preprocessing}:] Object of class \code{list} containing information about the pre-processing steps used on the raw data from this experiment
\item[\code{pubMedIds}:] Object of class \code{character} listing strings of PubMed identifiers of papers relevant to the dataset
\item[\code{other}:] Object of class \code{list} containing other information for which none of the above slots does not applies
}
\end{Section}
\begin{Section}{Methods}
Class-specific methods:
\describe{
\item[\code{abstract(MIAME)}:] An accessor function for \code{abstract}.
\item[\code{combine(MIAME,MIAME)}:] Combine two objects of \code{MIAME-class}, issuing warnings when ambiguities encountered.
\item[\code{expinfo(MIAME)}:] An accessor function for \code{name}, \code{lab}, \code{contact}, \code{title}, and \code{url}.
\item[\code{hybridizations(MIAME)}:] An accessor function for \code{hybridizations}.
\item[\code{normControls(MIAME)}:] An accessor function for \code{normControls}.
\item[\code{notes(MIAME), notes(MIAME) <- value}:] Accessor functions for \code{other}. \code{notes(MIAME) <- character}
\emph{appends} character to notes; use \code{notes(MIAME) <- list} to replace the notes entirely.
\item[\code{otherInfo(MIAME)}:] An accessor function for \code{other}.
\item[\code{preproc(MIAME)}:] An accessor function for \code{preprocessing}.
\item[\code{pubMedIds(MIAME), pubMedIds(MIAME) <- value}:] Accessor function for \code{pubMedIds}.
\item[\code{samples(MIAME)}:] An accessor function for \code{samples}.
}
Standard generic methods:
\describe{
\item[\code{updateObject(object, ..., verbose=FALSE)}] Update instance to current version, if necessary. See \code{\LinkA{updateObject}{updateObject}}
\item[\code{isCurrent(object)}] Determine whether version of object is current. See \code{\LinkA{isCurrent}{isCurrent}}
\item[\code{isVersioned(object)}] Determine whether object contains a 'version' string describing its structure . See \code{\LinkA{isVersioned}{isVersioned}}
\item[\code{show(MIAME)}:] Renders information about the MIAME information 
}
\end{Section}
\begin{Author}\relax
Rafael A. Irizarry
\end{Author}
\begin{References}\relax
\url{http://www.mged.org/Workgroups/MIAME/miame_1.1.html}
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{class:characterORMIAME}{class:characterORMIAME}}, \code{\LinkA{read.MIAME}{read.MIAME}}
\end{SeeAlso}

