\HeaderA{ExprTreeSet-class}{Class ExprTreeSet}{ExprTreeSet.Rdash.class}
\aliasA{attachExpr,ExprTreeSet-method}{ExprTreeSet-class}{attachExpr,ExprTreeSet.Rdash.method}
\aliasA{exprs,ExprTreeSet-method}{ExprTreeSet-class}{exprs,ExprTreeSet.Rdash.method}
\aliasA{exprs<-,ExprTreeSet,data.frame-method}{ExprTreeSet-class}{exprs<.Rdash.,ExprTreeSet,data.frame.Rdash.method}
\aliasA{ExprTreeSet}{ExprTreeSet-class}{ExprTreeSet}
\aliasA{exprType}{ExprTreeSet-class}{exprType}
\aliasA{exprType,ExprTreeSet-method}{ExprTreeSet-class}{exprType,ExprTreeSet.Rdash.method}
\aliasA{exprType<\Rdash}{ExprTreeSet-class}{exprType<.Rdash.}
\aliasA{exprType<-,ExprTreeSet,character-method}{ExprTreeSet-class}{exprType<.Rdash.,ExprTreeSet,character.Rdash.method}
\aliasA{mvaplot,ExprTreeSet-method}{ExprTreeSet-class}{mvaplot,ExprTreeSet.Rdash.method}
\aliasA{normType}{ExprTreeSet-class}{normType}
\aliasA{normType,ExprTreeSet-method}{ExprTreeSet-class}{normType,ExprTreeSet.Rdash.method}
\aliasA{normType<\Rdash}{ExprTreeSet-class}{normType<.Rdash.}
\aliasA{normType<-,ExprTreeSet,character-method}{ExprTreeSet-class}{normType<.Rdash.,ExprTreeSet,character.Rdash.method}
\aliasA{removeExpr,ExprTreeSet-method}{ExprTreeSet-class}{removeExpr,ExprTreeSet.Rdash.method}
\aliasA{se.exprs}{ExprTreeSet-class}{se.exprs}
\aliasA{se.exprs,ExprTreeSet-method}{ExprTreeSet-class}{se.exprs,ExprTreeSet.Rdash.method}
\aliasA{xpsNormalize,ExprTreeSet-method}{ExprTreeSet-class}{xpsNormalize,ExprTreeSet.Rdash.method}
\aliasA{xpsPreFilter,ExprTreeSet-method}{ExprTreeSet-class}{xpsPreFilter,ExprTreeSet.Rdash.method}
\aliasA{xpsUniFilter,ExprTreeSet-method}{ExprTreeSet-class}{xpsUniFilter,ExprTreeSet.Rdash.method}
\keyword{classes}{ExprTreeSet-class}
\begin{Description}\relax
This class provides the link to the \code{\LinkA{ROOT}{ROOT}} expression file and 
the \code{\LinkA{ROOT}{ROOT}} trees contained therein. It extends class \code{\LinkA{ProcesSet}{ProcesSet}}.
\end{Description}
\begin{Section}{Objects from the Class}
Objects are created using functions \code{\LinkA{express}{express}}, \code{\LinkA{summarize}{summarize}} 
or \code{\LinkA{normalize}{normalize}}, or the specialized functions \code{\LinkA{rma}{rma}}, \code{\LinkA{mas5}{mas5}} 
or \code{\LinkA{mas4}{mas4}}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{exprtype}:] Object of class \code{"character"} representing the exression type, 
i.e. \sQuote{rma}, \sQuote{mas5}, \sQuote{mas4} or \sQuote{custom}.
\item[\code{normtype}:] Object of class \code{"character"} representing the normalization 
type, i.e. \sQuote{mean}, \sQuote{median}, \sQuote{lowess},\sQuote{supsmu}.
\item[\code{scheme}:] Object of class \code{"SchemeTreeSet"} providing access to 
\code{\LinkA{ROOT}{ROOT}} scheme file.
\item[\code{data}:] Object of class \code{"data.frame"}. The data.frame can contain 
the data (e.g. expression levels) stored in \code{\LinkA{ROOT}{ROOT}} data trees.
\item[\code{params}:] Object of class \code{"list"} representing relevant parameters.
\item[\code{setname}:] Object of class \code{"character"} representing the name to the
\code{\LinkA{ROOT}{ROOT}} file subdirectoy where the \code{\LinkA{ROOT}{ROOT}} data trees are stored,
usually \sQuote{PreprocesSet}.
\item[\code{settype}:] Object of class \code{"character"} describing the type of treeset
stored in \code{setname}, usually \sQuote{preprocess}.
\item[\code{rootfile}:] Object of class \code{"character"} representing the name 
of the \code{\LinkA{ROOT}{ROOT}} data file, including full path.
\item[\code{filedir}:] Object of class \code{"character"} describing the full path to
the system directory where \code{rootfile} is stored.
\item[\code{numtrees}:] Object of class \code{"numeric"} representing the number of 
\code{\LinkA{ROOT}{ROOT}} trees stored in subdirectoy \code{setname}.
\item[\code{treenames}:] Object of class \code{"list"} representing the names of the 
\code{\LinkA{ROOT}{ROOT}} trees stored in subdirectoy \code{setname}.
}
\end{Section}
\begin{Section}{Extends}
Class \code{"\LinkA{ProcesSet}{ProcesSet.Rdash.class}"}, directly.
Class \code{"\LinkA{TreeSet}{TreeSet.Rdash.class}"}, by class "ProcesSet", distance 2.
\end{Section}
\begin{Section}{Methods}
\describe{
\item[attachExpr] \code{signature(object = "ExprTreeSet")}: exports expression trees from 
\code{\LinkA{ROOT}{ROOT}} expression file and and saves as data.frame \code{data}.
\item[exprType] \code{signature(object = "ExprTreeSet")}: extracts slot \code{exprtype}.
\item[exprType<-] \code{signature(object = "ExprTreeSet", value = "character")}: replaces slot \code{exprtype}.
\item[exprs] \code{signature(object = "ExprTreeSet")}: extracts the expression data.frame.
\item[exprs<-] \code{signature(object = "ExprTreeSet", value = "data.frame")}: replaces the expression data.frame.
\item[mvaplot] \code{signature(x = "ExprTreeSet")}: creates an MvA-plot.
\item[normType] \code{signature(object = "ExprTreeSet")}: extracts slot \code{normtype}.
\item[normType<-] \code{signature(object = "ExprTreeSet", value = "character")}: replaces slot \code{normtype}.
\item[removeExpr] \code{signature(object = "ExprTreeSet")}: replaces data.frame \code{data} 
with an empty data.frame of dim(0,0).
\item[se.exprs] \code{signature(object = "ExprTreeSet")}: extracts the standard deviation data.frame.
\item[xpsNormalize] \code{signature(object = "ExprTreeSet")}: applies normalization methods.
\item[xpsPreFilter] \code{signature(object = "ExprTreeSet")}: applies prefiltering methods.
\item[xpsUniFilter] \code{signature(object = "ExprTreeSet")}: applies unifiltering methods.
}
\end{Section}
\begin{Author}\relax
Christian Stratowa
\end{Author}
\begin{SeeAlso}\relax
related classes \code{\LinkA{DataTreeSet}{DataTreeSet.Rdash.class}}, \code{\LinkA{CallTreeSet}{CallTreeSet.Rdash.class}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
showClass("ExprTreeSet")
\end{ExampleCode}
\end{Examples}

