\HeaderA{maigesDEcluster-class}{maigesDEcluster class, store results of differential gene expression
analysis}{maigesDEcluster.Rdash.class}
\aliasA{maigesDEcluster}{maigesDEcluster-class}{maigesDEcluster}
\keyword{classes}{maigesDEcluster-class}
\begin{Description}\relax
This class extends the class \code{\LinkA{maigesDE}{maigesDE}} to store results
from differential expression analysis. It is produced in the same way
as the latter, but has one more slot containing the W values. This is
useful to do cluster analysis. Together the slots of the
\code{\LinkA{maigesDE}{maigesDE}} class, it has one more given in \emph{Slots} section.
\end{Description}
\begin{Details}\relax
Objects of this class are produced  in the same way as
\code{\LinkA{maigesDE}{maigesDE}}. The addition of the slot \code{W} turn
possible to do cluster analysis in this class of objects using the
functions \code{\LinkA{hierMde}{hierMde}}, \code{\LinkA{somMde}{somMde}} and
\code{\LinkA{kmeansMde}{kmeansMde}}, selecting genes according to the results of gene
expression analysis.
\end{Details}
\begin{Section}{Slots}
\describe{
\item[\code{W}:] numeric matrix containing the W values for the
genes and samples used in the analysis.
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[boxplot] \code{signature(x = 'maigesDEcluster')}: boxplot method for
\code{\LinkA{maigesDEcluster}{maigesDEcluster}} class. Display boxplots of one gene
previously defined.
\item[plot] \code{signature(x = 'maigesDEcluster')}: plot method for
\code{\LinkA{maigesDEcluster}{maigesDEcluster}} class. Display \emph{MA} plots.
\item[print] \code{signature(x = 'maigesDEcluster')}: print method for
\code{\LinkA{maigesDEcluster}{maigesDEcluster}} class.
\item[show] \code{signature(x = 'maigesDEcluster')}: show method for
\code{\LinkA{maigesDEcluster}{maigesDEcluster}} class.
\item[summary] \code{signature(x = 'maigesDEcluster')}: summary method for
\code{\LinkA{maigesDEcluster}{maigesDEcluster}} class.
}
\end{Section}
\begin{Author}\relax
Gustavo H. Esteves <\email{gesteves@vision.ime.usp.br}>
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{deGenes2by2Ttest}{deGenes2by2Ttest}}, \code{\LinkA{deGenes2by2Wilcox}{deGenes2by2Wilcox}},
\code{\LinkA{deGenes2by2BootT}{deGenes2by2BootT}}, \code{\LinkA{deGenesANOVA}{deGenesANOVA}},
\code{\LinkA{hierMde}{hierMde}}, \code{\LinkA{somMde}{somMde}}, \code{\LinkA{kmeansMde}{kmeansMde}}.
\end{SeeAlso}

