\HeaderA{ExpressionSetList-class}{A class for containing a list of ExpressionSets}{ExpressionSetList.Rdash.class}
\aliasA{.integrativeCorrelationFilter,ExpressionSetList-method}{ExpressionSetList-class}{.integrativeCorrelationFilter,ExpressionSetList.Rdash.method}
\aliasA{coerce,list,ExpressionSetList-method}{ExpressionSetList-class}{coerce,list,ExpressionSetList.Rdash.method}
\aliasA{featureNames,ExpressionSetList-method}{ExpressionSetList-class}{featureNames,ExpressionSetList.Rdash.method}
\aliasA{geneCenter,ExpressionSetList-method}{ExpressionSetList-class}{geneCenter,ExpressionSetList.Rdash.method}
\aliasA{lapply,ExpressionSetList-method}{ExpressionSetList-class}{lapply,ExpressionSetList.Rdash.method}
\aliasA{nrow,ExpressionSetList-method}{ExpressionSetList-class}{nrow,ExpressionSetList.Rdash.method}
\aliasA{nSamples}{ExpressionSetList-class}{nSamples}
\aliasA{nSamples,ExpressionSetList-method}{ExpressionSetList-class}{nSamples,ExpressionSetList.Rdash.method}
\aliasA{pca,ExpressionSetList-method}{ExpressionSetList-class}{pca,ExpressionSetList.Rdash.method}
\aliasA{pData,ExpressionSetList-method}{ExpressionSetList-class}{pData,ExpressionSetList.Rdash.method}
\aliasA{standardizeSamples,ExpressionSetList-method}{ExpressionSetList-class}{standardizeSamples,ExpressionSetList.Rdash.method}
\aliasA{studyCenter,ExpressionSetList-method}{ExpressionSetList-class}{studyCenter,ExpressionSetList.Rdash.method}
\aliasA{xapply,ExpressionSetList-method}{ExpressionSetList-class}{xapply,ExpressionSetList.Rdash.method}
\aliasA{zeroNu,ExpressionSetList-method}{ExpressionSetList-class}{zeroNu,ExpressionSetList.Rdash.method}
\aliasA{[,ExpressionSetList-method}{ExpressionSetList-class}{[,ExpressionSetList.Rdash.method}
\keyword{classes}{ExpressionSetList-class}
\begin{Description}\relax
Each element in the list must be a valid
\code{ExpressionSet}.  The \code{featureNames} must be identical for
each \code{ExpressionSet}.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("ExpressionSetList", ...)}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{.Data}:] Object of class \code{"list"}
}
\end{Section}
\begin{Section}{Extends}
Class \code{"\LinkA{list}{list.Rdash.class}"}, from data part.
Class \code{"\LinkA{vector}{vector.Rdash.class}"}, by class "list", distance 2.
Class \code{\LinkA{class.AssayData}{class.AssayData}}, by class "list", distance 2.
\end{Section}
\begin{Section}{Methods}
\describe{

\item[.integrativeCorrelationFilter] \code{signature(object =
  "ExpressionSetList")} Experimental function for filtering an arbitrary
list of ExpressionSets by integrative correlation.  Genes are excluded
that do not exceed the fdr threshold in at least 1 of the studies.

\item["["] \code{signature(x = "ExpressionSetList")} Subsets each
\code{ExpressionSet} element in the list.


\item[coerce] \code{signature(from = "list", to = "ExpressionSetList")}
Coerces a list of \code{ExpressionSet} objects to an object of class
\code{ExpressionSetList}. The \code{validityMethod} for the
\code{ExpressionSetList} class will return an error if the
\code{featureNames} for each \code{ExpressionSet} are not identical.

\item[featureNames] \code{signature(object = "ExpressionSetList")}
Accessor for the \code{featureNames}

\item[geneCenter] \code{signature(object = "ExpressionSetList")} See
\code{\LinkA{geneCenter}{geneCenter}}

\item[lapply] \code{signature(object="ExpresssionSetList")} Coerces
instance of ExpressionSetList to a list and does lapply on the list.
Returns an object of class ExpressionSetList

\item[nSamples] \code{signature(x = "ExpressionSetList")} Numerical
vector giving the number of samples in each \code{ExpressionSet}

\item[nrow] \code{signature(x = "ExpressionSetList")} Numerical: number
of features or genes

\item[pData] \code{signature(object = "ExpressionSetList")} returns a
list of \code{data.frames}.  The elements of the list correspond to
the studies in the \code{ExpressionSetList} object.

\item[.pca] \code{signature(object = "ExpressionSetList")} Runs
principal components to generate cross-study summary scores of
differential expression in multiple studies.  Not meant to be called
directly.  See \code{\LinkA{xsScores}{xsScores}}.

\item[standardizeSamples] \code{signature(object = "ExpressionSetList")}
See \code{\LinkA{standardizeSamples}{standardizeSamples}}


\item[studyCenter] \code{signature(object = "ExpressionSetList")}
See \code{\LinkA{studyCenter}{studyCenter}}


\item[xapply] \code{signature(object="ExpressionSetList")} An lapply for
\code{ExpressionSetList} instances.  See \code{\LinkA{xapply}{xapply}}.

\item[zeroNu] \code{signature(object = "ExpressionSetList")}
See \code{`\LinkA{zeroNu}{zeroNu}}. 
}
\end{Section}
\begin{Author}\relax
R. Scharpf
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{XdeMcmc-class}{XdeMcmc.Rdash.class}}, \code{\LinkA{XdeParameter-class}{XdeParameter.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
showClass("ExpressionSetList")
data(expressionSetList)
\end{ExampleCode}
\end{Examples}

