\HeaderA{transform.ProbeSet}{A function to transform a ProbeSet}{transform.ProbeSet}
\keyword{manip}{transform.ProbeSet}
\begin{Description}\relax
A function to transform the PMs and MMs in a ProbeSet.
\end{Description}
\begin{Usage}
\begin{verbatim}
## S3 method for class 'ProbeSet':
transform(`_data`, fun = I, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{\_data}] object of \code{\LinkA{ProbeSet-class}{ProbeSet.Rdash.class}}.
\item[\code{fun}] a function. The identity function by default.
\item[\code{...}] optional arguments for \code{fun}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The function \code{fun} is applied to the slots \code{pm} and \code{mm}.
The function \code{vsnh} in the package \code{vsn} is a recommended
argument for \code{fun}.
\end{Details}
\begin{Value}
An object of class \code{ProbeSet}.
\end{Value}
\begin{Note}\relax
This function should make to the package \code{affy} for the version 1.4.x.
\end{Note}
\begin{Author}\relax
Laurent
\end{Author}
\begin{Examples}
\begin{ExampleCode}
library(affydata)

data(Dilution)

ppset.name <- sample(featureNames(Dilution), 1)
ppset <- probeset(Dilution, ppset.name)[[1]]
ppset.log <- transform(ppset, fun=log)

par(mfrow=c(1,2))
plot(ppset)
plot(ppset.log)
\end{ExampleCode}
\end{Examples}

