\HeaderA{corParams}{Flag highly correlated parameters}{corParams}
\keyword{models}{corParams}
\begin{Description}\relax
Flags all highly correlated variables which model the same
data to reduce the number of variables and interactions in the model
calculation.
\end{Description}
\begin{Usage}
\begin{verbatim}
  corParams(pData) 
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{pData}] An object of class
\code{\LinkA{phenoData}{phenoData}} containing the
phenotypic information for the experiment.
\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{corParams}{corParams}} identifies variables
within the study design that are highly correlated and flags
them up for the user. These may represent different representations of
the same data and will affect model fitting, so should be removed from
the data set. Variables found to be highly correlated are suffixed
with the flags '*', '**', '***' etc.

\code{\LinkA{corParams}{corParams}} is an internal function and is not
designed to be accessed by users.
\end{Details}
\begin{Value}
A list is returned containing the following slots:

\begin{ldescription}
\item[\code{corParamNames}] A character vector of the names of the parameters
found to have very high correlation, suffixed with flags '*', '**',
'***' etc.
\item[\code{corParams}] A list containing the indices for variables found to
be highly correlated with one another.
\end{ldescription}
\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}

