\HeaderA{RefPlus-package}{RMA based on reference microarrays: RMA+ and RMA++ methods}{RefPlus.Rdash.package}
\aliasA{RefPlus}{RefPlus-package}{RefPlus}
\keyword{package}{RefPlus-package}
\begin{Description}\relax
RMA+ is an extenstion of the RMA algorithm that calculates the probeset 
intensities of a microarray using a pre-stored RMA model fitted on previously 
obtained microarrays, e.g. reference microarrays. RMA++ is a further extension 
based on the RMA+ method. This package depends on the affyPLM package.
\end{Description}
\begin{Details}\relax
\Tabular{ll}{
Package: & RefPlus\\
Type: & Package\\
Version: & 1.9.0\\
Date: & 2007-11-1\\
License: & GPL version 2 or newer\\
}
Use \code{rma.para} to obtain the reference quantiles and the probe effects from
a reference set, then use \code{rmaplus} to calculate the RMA+ intensities based 
on the fitted reference quantiles and probe effects.
\end{Details}
\begin{Author}\relax
By 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.Avaliable
with the package.

Harbron, C, Chang, K.M., South,M.C.(2007) RefPlus : an R package extending the 
RMA Algorithm. Bioinformatics 23, 2493-2494.
\end{References}
\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}

