\name{normalize.quantiles.robust}
\alias{normalize.quantiles.robust}
\alias{normalize.AffyBatch.quantiles.robust}
\title{Robust Quantile Normalization}
\description{Using a normalization based upon quantiles, this function
  normalizes a matrix of probe level intensities. Allows weighting of chips}
\usage{
      normalize.quantiles.robust(x,copy=TRUE,weights=NULL,
                remove.extreme=c("variance","mean","both","none"),
                n.remove=1,use.median=FALSE,use.log2=FALSE)
}

\arguments{
  \item{x}{A matrix of intensities, columns are chips, rows are probes}
  \item{copy}{Make a copy of matrix before normalizing. Usually safer to
    work with a copy}
  \item{weights}{A vector of weights, one for each chip}
  \item{remove.extreme}{If weights is null, then this will be used for
  determining which chips to remove from the calculation of the
  normalization distribution, See details for more info}
  \item{n.remove}{number of chips to remove}
  \item{use.median}{if TRUE use the median to compute normalization
    chip, otherwise uses a weighted mean}
  \item{use.log2}{work on log2 scale. This means we will be using the
    geometric mean rather than ordinary mean}
}
\details{This method is based upon the concept of a quantile-quantile 
  plot extended to n dimensions. Note that the matrix is of intensities
  not log intensities. The function performs better with raw
  intensities.
  
  Choosing \bold{variance} will remove chips with variances much higher
  or lower than the other chips, \bold{mean} removes chips with the mean
  most different from all the other means, \bold{both} removes first
  extreme variance and then an extreme mean. The option \bold{none} does
  not remove any chips, but will assign equal weights to all chips.

  Note that this function does not handle missing values (ie
  NA). Unexpected results might occur in this situation.
  
}
\note{This function is still experimental.}
\value{a matrix of normalized intensites}
\author{Ben Bolstad, \email{bmb@bmbolstad.com}}

\seealso{\code{\link{normalize.quantiles}}}
\keyword{manip}