\name{normalize.invariantset}
\alias{normalize.invariantset}
\alias{normalize.AffyBatch.invariantset}
\title{Invariante Set normalization}
\description{
Normalize arrays in an  \code{\link[affy:AffyBatch-class]{AffyBatch}} using an invariant set.
}
\usage{
normalize.AffyBatch.invariantset(abatch,
                   prd.td=c(0.003, 0.007), verbose=FALSE,baseline.type=c("mean","median","pseudo-mean","pseudo-median"),type=c("separate","pmonly","mmonly","together"))

normalize.invariantset(data, ref, prd.td=c(0.003,0.007))
}
\arguments{
  \item{abatch}{an \code{\link[affy:AffyBatch-class]{AffyBatch}}}
  \item{data}{a vector of intensities on a chip (to normalize to the reference).}
  \item{ref}{a vector of reference intensities.}
  \item{prd.td}{cutoff parameter (details in the bibliographic
    reference)}
  \item{baseline.type}{Specify how to determine the baseline array}
  \item{type}{A string specifying how the normalization should be
    applied. See details for more.}
  \item{verbose}{A flag to have a dumps throughout the normalization}
}
\value{
  Respectively a \code{\link[affy:AffyBatch-class]{AffyBatch}} of normalized objects, or
  a vector of normalized intensities, with an attribute "invariant.set"
  holding the indexes of the 'invariant' intensities.
}
\details{
  The set of invariant intensities between \code{data} and
  \code{ref} is found through an iterative
  process (based on the respective ranks the intensities).
  This set of intensities is used to generate a normalization curve by
  smoothing.

  The \code{type} argument should be one of
  \code{"separate","pmonly","mmonly","together"} which indicates whether
  to normalize only one probe type (PM,MM) or both together or separately.
  
}
\author{
  L. Gautier <laurent@cbs.dtu.dk>
  (Thanks to Cheng Li for the discussions about the algorithm.)
}
\references{
  Cheng Li and Wing Hung Wong, Model-based analysis of
  oligonucleotides arrays: model validation, design issues and
  standard error application. Genome Biology 2001, 2(8):research0032.1-0032.11
}
\seealso{
  \code{\link{normalize}} to normalize \code{\link[affy:AffyBatch-class]{AffyBatch}} objects.
}
\keyword{manip}