\HeaderA{dataTransform}{Gene expression data formatting for Envisage}{dataTransform}
\keyword{models}{dataTransform}
\begin{Description}\relax
Ensures that the gene expression data from the
\code{\LinkA{ExpressionSet}{ExpressionSet}} object is in
the correct format for package \pkg{Envisage}.
\end{Description}
\begin{Usage}
\begin{verbatim}
  dataTransform(expData)  
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{expData}] Object of class
\code{\LinkA{ExpressionSet}{ExpressionSet}} containing
gene expression data.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The \pkg{Envisage} package contains methods allowing the use of 
linear models (LMs) for analysing significantly changing genes in 
experiments with a variety of sources of variation, be they
experimentally controlled variables such as drug treatment or time, or
non-controlled sources of confounding variation such as phenotypic or
environmental differences. This allows all sources of variation to be
considered when analysing for significant differential expression,
ensuring resulting genes are biologically relevent to the experimental
question. 

The function \code{\LinkA{dataTransform}{dataTransform}} is an internal
function that ensures that the gene expression data (in the
form of an object of class
\code{\LinkA{ExpressionSet}{ExpressionSet}}) is in the
correct format for future processing. In particular, this function
ensures that data is in a logged format.

\code{\LinkA{dataTransform}{dataTransform}} is an internal function and is
not designed to be accessed by users.
\end{Details}
\begin{Value}
Returns a matrix of processed expression values (this may be very large).
\end{Value}
\begin{Author}\relax
Sam Robson \email{S.C.Robson@warwick.ac.uk}
\end{Author}
\begin{References}\relax
Robson, S. C., Hunter, E., Bird, H., Turner, H. (2008) 
\emph{Envisage: model-based significance analysis of microarray gene
expression data}, manuscript in preparation
\end{References}
\begin{SeeAlso}\relax
For the main \pkg{Envisage} method, see
\code{\LinkA{envisage}{envisage}}.
\end{SeeAlso}

