\HeaderA{justvsn}{Wrapper functions for vsn}{justvsn}
\aliasA{vsnrma}{justvsn}{vsnrma}
\begin{Description}\relax
\code{justvsn} returns the vsn-normalised intensities in
an object generally of the same class as its first
argument (see the man page of \code{\LinkA{predict}{predict}} for
details). It preserves the metadata. It is equivalent to calling
\begin{alltt}
  fit = vsn2(x, ...)
  nx = predict(fit, newdata=x, useDataInFit = TRUE)
\end{alltt}
\code{vsnrma} is a wrapper around \code{\LinkA{vsn2}{vsn2}} and \code{\LinkA{rma}{rma}}
\end{Description}
\begin{Usage}
\begin{verbatim}
justvsn(x, ...)
vsnrma(x, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] For \code{justvsn}, any kind of object for which
\code{\LinkA{vsn2}{vsn2}} methods exist.
For \code{vsnrma}, an
\code{\LinkA{AffyBatch}{AffyBatch}}.
\item[\code{...}] Further arguments that get passed on to \code{\LinkA{vsn2}{vsn2}}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\code{vsnrma} does probe-wise
background correction and between-array normalization by calling
\code{\LinkA{vsn2}{vsn2}} on the perfect match (PM) values only. Probeset
summaries are calculated with the medianpolish algorithm of
\code{\LinkA{rma}{rma}}.
\end{Details}
\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}
##--------------------------------------------------
## use "vsn2" to produce a "vsn" object
##--------------------------------------------------
data("kidney")
fit = vsn2(kidney)
nkid = predict(fit, newdata=kidney)

##--------------------------------------------------
## justvsn on ExpressionSet
##--------------------------------------------------
nkid2 = justvsn(kidney)
stopifnot(identical(exprs(nkid), exprs(nkid2)))

##--------------------------------------------------
## justvsn on AffyBatch
##--------------------------------------------------
data("affybatch.example")
data("cdfenv.example")
abe1 = justvsn(affybatch.example)
abe2 = vsnrma(affybatch.example)

##--------------------------------------------------
## justvsn on RGList
##--------------------------------------------------
rg = new("RGList", list(R=exprs(kidney)[,1,drop=FALSE], G=exprs(kidney)[,2,drop=FALSE]))
erge = justvsn(rg)
\end{ExampleCode}
\end{Examples}

