\HeaderA{normalize.quantiles2}{Reference quantile normalization}{normalize.quantiles2}
\keyword{manip}{normalize.quantiles2}
\begin{Description}\relax
Quantile normalization to a reference set.
\end{Description}
\begin{Usage}
\begin{verbatim}
normalize.quantiles2(X, Reference.Quantiles)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{X}] A matrix of probe intensity data to be reference quantile 
normalized.
\item[\code{Reference.Quantiles}] A vector of the reference quantiles that the probe 
intensities of a sample is normalized to.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The function quantile normalized the probe intensities of a set of microarrays
to a set of reference quantiles which are formed by a set of reference 
microarrays.
\end{Details}
\begin{Value}
The reference quantile normalized probe intensities.
\end{Value}
\begin{Author}\relax
Kai-Ming Chang(kaiming@gmail.com)
\end{Author}
\begin{References}\relax
Chang,K.M., Harbron,C., South,M.C. (2006) An Exploration of 
Extensions to the RMA Algorithm. Available with the RefPlus package.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{normalize.quantiles}{normalize.quantiles}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
A<-matrix(rnorm(30),10,3)
core<-1:10
An<-normalize.quantiles2(A,core)
rank(A[,1])==An[,1]
\end{ExampleCode}
\end{Examples}

