\name{normalize.ExpressionSet.gq}
\alias{normalize.ExpressionSet.gq}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{
gene quantiles normalization
}
\description{
Performs gene quantile normalization for cross-platform adjustments of microarray data. 
It is a modification of the median rank scores normalization.
}
\usage{
normalize.ExpressionSet.gq(ExpressionSet = NULL, Batch = NULL, ...)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
  \item{ExpressionSet}{
An ExpressionSet object; if it contains a "Batch" column in its pData slot, this information can be used instead of the "Batch" parameter.
}
  \item{Batch}{
A character or numeric vector containing batch contribution of the samples. 
The order of the items should be the same as the samples (column) in the supplied ExpressionSet.
Defining this parameter overrides the information of the pData slot.
}
  \item{\dots}{
Can be used to pass on parameters to underlying functions.
}
}
\details{
Please see the references for details.
}
\value{
An ExpressionSet object with adjusted expression matrix.
}
\references{
%% ~put references to the literature/web site here ~
Xia XQ, McClelland M, Porwollik S, Song W, Cong X, Wang Y: WebArrayDB: cross-platform microarray data analysis and public data repository. Bioinformatics 2009, 25:2425-2429.
}
\author{
Andreas Heider
}
\note{
%%  ~~further notes~~
}

%% ~Make other sections like Warning with \section{Warning }{....} ~

\seealso{
%% ~~objects to See Also as \code{\link{help}}, ~~~
virtualArrayExpressionSets
}
\examples{
# library(affydata)
# data(Dilution)
# Dilution <- rma(Dilution)
# normalize.ExpressionSet.gq(Dilution,Batch=c("A","B","A","B"))
}
% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.
\keyword{ virtualArray }
\keyword{ batch effect removal }
\keyword{ normalization }
\keyword{ cross-platform }