\HeaderA{vsnInput}{Class to contain input data and parameters for vsn functions}{vsnInput}
\aliasA{class:vsnInput}{vsnInput}{class:vsnInput}
\aliasA{dim,vsnInput-method}{vsnInput}{dim,vsnInput.Rdash.method}
\aliasA{ncol,vsnInput-method}{vsnInput}{ncol,vsnInput.Rdash.method}
\aliasA{nrow,vsnInput-method}{vsnInput}{nrow,vsnInput.Rdash.method}
\aliasA{show,vsnInput-method}{vsnInput}{show,vsnInput.Rdash.method}
\aliasA{vsnInput-class}{vsnInput}{vsnInput.Rdash.class}
\aliasA{[,vsnInput-method}{vsnInput}{[,vsnInput.Rdash.method}
\keyword{classes}{vsnInput}
\begin{Description}\relax
Class to contain input data and parameters for vsn functions
\end{Description}
\begin{Section}{Creating Objects}
\code{new("vsnInput")}
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{x}:] A numeric matrix with the input data.
\item[\code{reference}:] An object of \code{\LinkA{vsn}{vsn.Rdash.class}},
typically this would have been
obtained from a previous fit to a set of reference arrays (data).
\item[\code{strata}:] A factor of length 0 or n. If its length is
n, then its levels correspond to different normalization strata
(see \code{\LinkA{vsn2}{vsn2}}).
\item[\code{ordered}:] Logical scalar; are the rows reordered so that
the strata are contiguous.
\item[\code{lts.quantile}:] Numeric scalar, see\code{\LinkA{vsn2}{vsn2}}.
\item[\code{subsample}:] Integer scalar, see\code{\LinkA{vsn2}{vsn2}}.
\item[\code{verbose}:] Logical scalar, see\code{\LinkA{vsn2}{vsn2}}.
\item[\code{pstart}:] A 3D array of size (number of strata) x (number of
columns of the data matrix) x 2 containing start parameters.
\item[\code{cvg.niter}:] Integer scalar, see\code{\LinkA{vsn2}{vsn2}}.
\item[\code{cvg.eps}:] Numeric scalar, see\code{\LinkA{vsn2}{vsn2}}.
}
\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
}
\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}
\end{ExampleCode}
\end{Examples}

