\name{prep}
\alias{prep}
\title{Pre-process a matrix for PCA}
\usage{prep(object, scale=c("none", "pareto", "vector", "uv"),
    center=TRUE, eps=1e-12, simple=TRUE, reverse=FALSE, ...)}
\description{Scaling and centering a matrix.}
\details{Does basically the same as \code{\link{scale}} but adds some
alternative scaling options and functionality for treating
pre-processing as part of a model.}
\value{A pre-processed matrix or a list with
\item{center}{a vector with the estimated centers}
\item{scale}{a vector with the estimated scales}
\item{data}{the pre (or post) processed data}}
\author{Henning Redestig}
\arguments{\item{object}{Numerical matrix (or an object coercible to such)
with samples in rows and variables as columns. Also takes
\code{ExpressionSet} in which case the transposed expression
matrix is used.}
\item{scale}{One of "UV" (unit variance \eqn{a=a/\sigma_{a}})
"vector" (vector normalisation \eqn{b=b/||b||}), "pareto" (sqrt
UV) or "none" to indicate which scaling should be used to scale
the matrix with \eqn{a} variables and \eqn{b} samples. Can also be
a vector of scales which should be used to scale the
matrix. \code{NULL} value is interpreted as \code{"none"}.}
\item{center}{Either a logical which indicates if the matrix
should be mean centred or not, or a vector with averages which
should be suntracted from the matrix. \code{NULL} value is
interpreted as \code{FALSE}}
\item{eps}{Minimum variance, variable with lower variance are not
scaled and warning is issued instead.}
\item{simple}{Logical indicating if only the data should be
returned or a list with the pre-processing statistics as well.}
\item{reverse}{Logical indicating  if matrix should be
'post-processed' instead by multiplying each column with its scale
and adding the center. In this case, center and scale should be
vectors with the statistics (no warning is issued if not, instead
output becomes the same as input).}
\item{...}{Only used for passing through arguments.}}
\examples{object <- matrix(rnorm(50), nrow=10)
res <- prep(object, scale="uv", center=TRUE, simple=FALSE)
obj <- prep(object, scale=res$scale, center=res$center)
## same as original
sum((object - prep(obj, scale=res$scale, center=res$center, rev=TRUE))^2)}