\HeaderA{normalize.quantiles.in.blocks}{Quantile Normalization carried out separately within blocks of rows}{normalize.quantiles.in.blocks}
\keyword{manip}{normalize.quantiles.in.blocks}
\begin{Description}\relax
Using a normalization based upon quantiles this function
normalizes the columns of a matrix such that different subsets of rows
get normalized together.
\end{Description}
\begin{Usage}
\begin{verbatim}
  normalize.quantiles.in.blocks(x,blocks,copy=TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] A matrix of intensities where each column corresponds to a
chip and each row is a probe.
\item[\code{copy}] Make a copy of matrix before normalizing. Usually safer to
work with a copy
\item[\code{blocks}] A vector giving block membership for each each row
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This method is based upon the concept of a quantile-quantile
plot extended to n dimensions. No special allowances are made for
outliers. If you make use of quantile normalization either through
\code{\LinkA{rma}{rma}} or \code{\LinkA{expresso}{expresso}}
please cite Bolstad et al, Bioinformatics (2003).
\end{Details}
\begin{Value}
From \code{normalize.quantiles.use.target} a normalized \code{matrix}.
\end{Value}
\begin{Author}\relax
Ben Bolstad, \email{bmb@bmbolstad.com}
\end{Author}
\begin{References}\relax
Bolstad, B (2001) \emph{Probe Level Quantile Normalization of High Density
Oligonucleotide Array Data}. Unpublished manuscript
\url{http://bmbolstad.com/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://bmbolstad.com/misc/normalize/normalize.html}
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{normalize}{normalize}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
   ### setup the data
   blocks <- c(rep(1,5),rep(2,5),rep(3,5))
   par(mfrow=c(3,2))
   x <- matrix(c(rexp(5,0.05),rnorm(5),rnorm(5,10)))
   boxplot(x ~ blocks)
   y <- matrix(c(-rexp(5,0.05),rnorm(5,10),rnorm(5)))
   boxplot(y ~ blocks)
   pre.norm <- cbind(x,y)

   ### the in.blocks version
   post.norm <- normalize.quantiles.in.blocks(pre.norm,blocks)
   boxplot(post.norm[,1] ~ blocks)
   boxplot(post.norm[,2] ~ blocks)

   ### the usual version
   post.norm  <- normalize.quantiles(pre.norm)
   boxplot(post.norm[,1] ~ blocks)
   boxplot(post.norm[,2] ~ blocks)
 \end{ExampleCode}
\end{Examples}