\HeaderA{xde}{Fit the Bayesian hierarchical model for cross-study differential
gene expression}{xde}
\keyword{models}{xde}
\keyword{multivariate}{xde}
\begin{Description}\relax
Fits the Bayesian hierarchical model for cross-study differential
gene expression.
\end{Description}
\begin{Usage}
\begin{verbatim}
  
  xde(paramsMcmc, esetList, outputMcmc)

\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{paramsMcmc}] Object of class \code{XdeParameter}
\item[\code{esetList}] Object of class \code{ExpressionSetList}
\item[\code{outputMcmc}] Object of class \code{XdeMcmc} (optional)
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Details for fitting the Bayesian model are discussed elsewhere (see
citation below and XdeParameterClass vignette)
\end{Details}
\begin{Value}
Object of class \code{XdeMcmc}
\end{Value}
\begin{Note}\relax
See the vignettes for XdeParameterClass and XDE.
\end{Note}
\begin{Author}\relax
R. Scharpf
\end{Author}
\begin{References}\relax
R. Scharpf et al., A Bayesian Model for Cross-Study Differential Gene
Expression, Technical Report 158, Johns Hopkins University, Department
of Biostatistics, 2007
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{XdeMcmc-class}{XdeMcmc.Rdash.class}}, \code{\LinkA{XdeParameter-class}{XdeParameter.Rdash.class}}, \code{\LinkA{ExpressionSetList-class}{ExpressionSetList.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Not run: 
  data(expressionSetList)
  xparam <- new("XdeParameter", phenotypeLabel="adenoVsquamous", esetList=expressionSetList)
  iterations(xparam) <- 10
  fit <- xde(xparam, esetList=expressionSetList)
## End(Not run)
\end{ExampleCode}
\end{Examples}

