\HeaderA{deGenesANOVA}{Function to do differential expression analysis, using ANOVA models}{deGenesANOVA}
\keyword{methods}{deGenesANOVA}
\begin{Description}\relax
This function takes an object of class \code{\LinkA{maiges}{maiges}} and do
differential expression analysis for the genes onto dataset, comparing
more than two samples using ANalysis Of VAriance (ANOVA)
models.
\end{Description}
\begin{Usage}
\begin{verbatim}
deGenesANOVA(data=NULL, eBayes=FALSE, retOrig=FALSE,
             retF=FALSE, doClust=TRUE, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{data}] object of class \code{\LinkA{maigesANOVA}{maigesANOVA}}.
\item[\code{eBayes}] logical indicating the use or not (default) of empirical
Bayes statistics implemented in \emph{limma} package.
\item[\code{retOrig}] logical indicating if the object of class
\code{\LinkA{MArrayLM}{MArrayLM}} from \emph{limma} package must be
returned. Defaults to FALSE.
\item[\code{retF}] logical asking to return the results associated with the
F test (TRUE) or with the individual contrasts (FALSE - default).
\item[\code{doClust}] logical indicating if the object generated from this
analysis will be used for cluster analysis. Defaults to TRUE.
\item[\code{...}] additional parameters to function \code{\LinkA{lmFit}{lmFit}}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The object of class \code{\LinkA{maigesANOVA}{maigesANOVA}} of the argument
\code{data} is created by the function \code{\LinkA{designANOVA}{designANOVA}}. This
function calculate statistics and p-values using the function
\code{\LinkA{lmFit}{lmFit}} from package \emph{limma}.
\end{Details}
\begin{Value}
The result of this function is an object of class
\code{\LinkA{MArrayLM}{MArrayLM}} when \code{retOrig} is TRUE. When it is
FALSE, the result is an object of class \code{\LinkA{maigesDE}{maigesDE}} if
\code{doClust} if FALSE or of class \code{\LinkA{maigesDEcluster}{maigesDEcluster}} if
it is TRUE.
\end{Value}
\begin{Author}\relax
Gustavo H. Esteves <\email{gesteves@vision.ime.usp.br}>
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{designANOVA}{designANOVA}}, \code{\LinkA{lmFit}{lmFit}}, \code{\LinkA{MArrayLM}{MArrayLM}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Loading the dataset
data(gastro)

## Constructing a maigesANOVA object for the 'Tissue' sample label using
## default model (simple linear model with intercept) and contrasts (all
## parameters are equal between themselves)
gastro.ANOVA = designANOVA(gastro.summ, factors="Tissue")

## Fitting the ANOVA model designed by the above command
gastro.ANOVAfit = deGenesANOVA(gastro.ANOVA, retF=TRUE)
gastro.ANOVAfit
\end{ExampleCode}
\end{Examples}

