\HeaderA{vsn}{Class to contain result of a vsn fit}{vsn}
\aliasA{class:vsn}{vsn}{class:vsn}
\aliasA{coef,vsn-method}{vsn}{coef,vsn.Rdash.method}
\aliasA{coefficients,vsn-method}{vsn}{coefficients,vsn.Rdash.method}
\aliasA{dim,vsn-method}{vsn}{dim,vsn.Rdash.method}
\aliasA{exprs,vsn-method}{vsn}{exprs,vsn.Rdash.method}
\aliasA{ncol,vsn-method}{vsn}{ncol,vsn.Rdash.method}
\aliasA{nrow,vsn-method}{vsn}{nrow,vsn.Rdash.method}
\aliasA{show,vsn-method}{vsn}{show,vsn.Rdash.method}
\aliasA{vsn-class}{vsn}{vsn.Rdash.class}
\aliasA{[,vsn-method}{vsn}{[,vsn.Rdash.method}
\keyword{classes}{vsn}
\begin{Description}\relax
Class to contain result of a vsn fit
\end{Description}
\begin{Section}{Creating Objects}
\code{new("vsn")}
\code{vsn2(x)} with \code{x} being an \code{\LinkA{ExpressionSet}{ExpressionSet}}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{coefficients}:] A 3D array of size (number of strata) x (number of
columns of the data matrix) x 2 containing fitted normalization parameters
(see vignette).
\item[\code{strata}:] A factor of length 0 or n. If its length is
n, then its levels correspond to different normalization strata
(see vignette).
\item[\code{mu}:] A numeric vector of length n with the fitted
parameters $\hat{\mu}_k$, $k=1,...,n$.
\item[\code{sigsq}:] A numeric scalar, $\hat{\sigma}$.
\item[\code{hx}:] A numeric matrix with 0 or n rows. If the number of
rows is n, then \code{hx} contains the transformed data matrix.
\item[\code{lbfgsb}:] An integer scalar containing the return code
from the L-BFGS-B optimizer.
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[\code{[}] Subset
\item[\code{dim}] Get dimensions of data matrix.
\item[\code{nrow}] Get number of rows of data matrix.
\item[\code{ncol}] Get number of columns of data matrix.
\item[\code{show}] Print a summary of the object
\item[\code{exprs}] Accessor to slot \code{hx}.
\item[\code{coef}, \code{coefficients}] Accessors to slot \code{coefficients}.
}
\end{Section}
\begin{Author}\relax
Wolfgang Huber \url{http://www.ebi.ac.uk/huber}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{vsn2}{vsn2}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  data("kidney")
  v = vsn2(kidney)
  show(v)
  dim(v)
  v[1:10, ]
\end{ExampleCode}
\end{Examples}

