\HeaderA{alias.glmNA}{Find Aliases (Dependencies) in a Model}{alias.glmNA}
\keyword{models}{alias.glmNA}
\begin{Description}\relax
Find aliases (linearly dependent terms) in a linear model
specified by a formula. This extends the S3 method
\code{\LinkA{alias}{alias}} to objects of class
\code{\LinkA{glmNA}{glmNA}} for package \pkg{Envisage}.
\end{Description}
\begin{Usage}
\begin{verbatim}
  ## S3 method for class 'glmNA':
  alias(object, ...) 
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] A fitted model object of class
\code{\LinkA{glmNA}{glmNA}}.
\item[\code{...}] Further arguments passed to or from other methods.
\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{alias.glmNA}{alias.glmNA}} extends the method
\code{\LinkA{alias}{alias}} to the S4 class
\code{\LinkA{glmNA}{glmNA}} for package
\pkg{Envisage}. This is an extension of classes \code{glm} and
\code{lm} and deals appropriately with genes that produce NA calls in
the modelling procedure. This allows use of the function
\code{\LinkA{Anova}{Anova}} for calculating significance for each gene. 

\code{\LinkA{alias.glmNA}{alias.glmNA}} is an internal function and is not
designed to be accessed by users.
\end{Details}
\begin{Value}
A list (of class "listof") containing components:

\begin{ldescription}
\item[\code{Model}] Description of the model; usually the formula.
\item[\code{Complete}] A matrix with columns corresponding to effects that
are linearly dependent on the rows.
\item[\code{Partial}] The correlations of the estimable effects, with a zero
diagonal. An object of class "mtable" which has its own print
method.
\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
\code{\LinkA{coef}{coef}}, \code{\LinkA{glmNA}{glmNA}. For the main \bsl{}pkg\{Envisage\} method, see
  \bsl{}code\{\LinkA{glmNA}{glmNA}\}.}
\end{SeeAlso}

