\HeaderA{normalize.quantiles.probeset}{Quantile Normalization applied to probesets}{normalize.quantiles.probeset}
\aliasA{normalize.AffyBatch.quantiles.probeset}{normalize.quantiles.probeset}{normalize.AffyBatch.quantiles.probeset}
\keyword{manip}{normalize.quantiles.probeset}
\begin{Description}\relax
Using a normalization based upon quantiles, this function
normalizes a matrix of probe level intensities.
\end{Description}
\begin{Usage}
\begin{verbatim}
  normalize.AffyBatch.quantiles.probeset(abatch,type=c("separate","pmonly","mmonly","together"),use.median=FALSE,use.log=TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{abatch}] An \code{\LinkA{AffyBatch}{AffyBatch}}
\item[\code{type}] how should MM and PM values be handled
\item[\code{use.median}] use median rather than mean
\item[\code{use.log}] take logarithms, then normalize
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function applies the \LinkA{quantile}{quantile} method in a probeset specific manner.

In particular a probeset summary is normalized using the quantile
method and then the probes adjusted accordingly.
\end{Details}
\begin{Value}
A normalized \code{AffyBatch}.
\end{Value}
\begin{Author}\relax
Ben Bolstad, \email{bolstad@stat.berkeley.edu}
\end{Author}
\begin{References}\relax
Bolstad, B (2001) \emph{Probe Level Quantile Normalization of High Density
Oligonucleotide Array Data}. Unpublished manuscript
\url{http://oz.berkeley.edu/~bolstad/stuff/qnorm.pdf}

Bolstad, B. M., Irizarry R. A., Astrand, M, and Speed, T. P. (2003)
\emph{A Comparison of Normalization Methods for High Density
Oligonucleotide Array Data Based on Bias and Variance.}
Bioinformatics 19(2) ,pp 185-193. \url{http://www.stat.berkeley.edu/~bolstad/normalize/normalize.html}
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{normalize}{normalize}}, \code{\LinkA{normalize.quantiles}{normalize.quantiles}}
\end{SeeAlso}

