\Header{rmaPLM}{Fit a RMA to Affymetrix Genechip Data as a PLMset}
\keyword{manip}{rmaPLM}
\begin{Description}\relax
This function converts an \code{\Link{AffyBatch}} into an
\code{\Link{PLMset}} by fitting a multichip model. In particular we
concentrate on the RMA model.
\end{Description}
\begin{Usage}
\begin{verbatim}
rmaPLM(object,normalize=TRUE,background=TRUE,background.method="RMA.2",normalize.method="quantile",background.param = list(),normalize.param=list(),output.param=list(),model.param=list())
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] an \code{\Link{AffyBatch}}
\item[\code{normalize}] logical value. If \code{TRUE} normalize data using
quantile normalization
\item[\code{background}] logical value. If \code{TRUE} background correct
using RMA background correction
\item[\code{background.method}] name of background method to use.
\item[\code{normalize.method}] name of normalization method to use.
\item[\code{background.param}] A list of parameters for background routines
\item[\code{normalize.param}] A list of parameters for normalization
routines
\item[\code{output.param}] A list of parameters controlling optional output
from the routine.
\item[\code{model.param}] A list of parameters controlling model procedure
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function fits the RMA as a Probe Level Linear models to all the probesets in
an \code{\Link{AffyBatch}}.
\end{Details}
\begin{Value}
An \code{\Link{PLMset}}
\end{Value}
\begin{Author}\relax
Ben Bolstad \email{bolstad@stat.berkeley.edu}
\end{Author}
\begin{References}\relax
Under Preparation
\end{References}
\begin{SeeAlso}\relax
\code{\Link{express}},\code{\Link{expresso}},
\code{\Link{rma}}, \code{\Link{threestep}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# A larger example testing weight image function
data(Dilution)
Pset <- rmaPLM(Dilution,output.param=list(weights=TRUE))
image(Pset)
\end{ExampleCode}
\end{Examples}

