\HeaderA{rmaplus}{Derive RMA+ intensities}{rmaplus}
\keyword{manip}{rmaplus}
\begin{Description}\relax
Calculate the RMA+ intensities using pre-stored reference quantiles and probe
effects. The reference quantiles and the probe effects are the estimated 
parameter values from RMAing a set of microarrays (e.g. a reference set).
\end{Description}
\begin{Usage}
\begin{verbatim}
rmaplus(Future, rmapara, r.q, p.e, bg = TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{Future}] An \code{affybatch} object of the microarrays to be 
pre-processed using the RMA+ methods.
\item[\code{rmapara}] Output of \code{rma.para} function that the contain reference 
quantiles and the reference probe effects.
\item[\code{r.q}] The pre-stored vector of the quantiles that the 
probe intensity data of a microarray should be normalized to.
\item[\code{p.e}] A pre-stored list of probe effects. It is a probe.coefs object of 
PLMset class in \code{affyPLM} package.
\item[\code{bg}] A logical flag. If \code{True}(by default), background correct 
\code{Train} using default \code{bg.correct.rma}. 
\end{ldescription}
\end{Arguments}
\begin{Value}
The RMA+ intensities of \code{Future}.
\end{Value}
\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{PLMset-class}{PLMset.Rdash.class}},\code{\LinkA{rma.para}{rma.para}},
\code{\LinkA{rmaref.predict}{rmaref.predict}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
if (require(affydata)) {
  ## Use Dilution in affydata package
  data(Dilution)

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

  ## Background correct, estimate the probe effects, and calculate the 
  ## RMA intensities using rma.para function.
  Para<-rma.para(Dilution,bg=TRUE,exp=TRUE)
  Ex1<-Para[[3]]

  ## Calculate the RMA+ intensity using rmaplus function. 
  Ex2<-rmaplus(Dilution, rmapara=Para, bg = TRUE)
}
\end{ExampleCode}
\end{Examples}

