\name{RefPlus-package}
\alias{RefPlus-package}
\alias{RefPlus}
\docType{package}
\title{
RMA based on reference microarrays: RMA+ and RMA++ methods
}
\description{
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. 
}

\details{
\tabular{ll}{
Package: \tab RefPlus\cr
Type: \tab Package\cr
Version: \tab 1.13.2\cr
Date: \tab 2009-03-11\cr
License: \tab GPL version 2 or newer\cr
}
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.
}
\author{
By Kai-Ming Chang(kaiming@gmail.com)
}
\references{
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.

}
\keyword{package}
\examples{
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)
}
}