\HeaderA{rma.para}{Fitting a RMA model}{rma.para}
\keyword{manip}{rma.para}
\begin{Description}\relax
Obtain reference quantiles and reference probe effects based on reference set 
Train, and calculate the gene expression
\end{Description}
\begin{Usage}
\begin{verbatim}
rma.para(Train, bg = TRUE, exp = FALSE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{Train}] An \code{AffyBatch} object of the reference set microarrays.
\item[\code{bg}] A logical flag. If \code{True}(by default), background correct 
\code{Train} using default \code{bg.correct.rma}. 
\item[\code{exp}] A logical flag. If \code{True}, calculate the RMA measurements of
\code{Train}. If \code{False}, return 0.
\end{ldescription}
\end{Arguments}
\begin{Value}
\begin{ldescription}
\item[\code{Reference.Quantiles}] Reference quantiles derived from \code{Train}.
\item[\code{probe.effects}] Estimated probe effects derived from \code{Train}.
\item[\code{expression}] RMA measurements of \code{Train}.
\end{ldescription}
\end{Value}
\begin{Note}\relax
The RMA procedure requires a lot of computer memory.
\end{Note}
\begin{Author}\relax
Kai-Ming Chang(kaiming@gmail.com)
\end{Author}
\begin{References}\relax
Chang,K.M., Harbron,C., South,M.C. (2006) An Exploration of 
Extensions to the RMA Algorithm. Available with the RefPlus package.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{rmaplus}{rmaplus}},\code{\LinkA{rmaref.predict}{rmaref.predict}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
if (require(affydata)) {
  ## Use Dilution in affydata package
  data(Dilution)

  ## Background correct, estimate the probe effects, and calculate the 
  ## RMA intensities using rma.para function.
  Ex<-rma.para(Dilution, bg=TRUE,exp=TRUE)

  ## Calculate the rma intensities using rma function.
  Ex0<-exprs(rma(Dilution))

  plot(Ex$express[,1],Ex0[,1])
}
\end{ExampleCode}
\end{Examples}

