\name{normalize.invariantset}
\alias{normalize.invariantset}
\alias{normalize.AffyBatch.invariantset}
\title{Invariant 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}} object.}
  \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}{specifies how to determine the baseline array.}
  \item{type}{a string specifying how the normalization should be
    applied. See details for more.}
  \item{verbose}{logical indicating printing 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}