\HeaderA{maigesDE-class}{maigesDE class, store results of differential gene expression
analysis}{maigesDE.Rdash.class}
\aliasA{maigesDE}{maigesDE-class}{maigesDE}
\keyword{classes}{maigesDE-class}
\begin{Description}\relax
This class defines a structure to store the results from differential
expression analysis. This type of analysis can be done using the
functions \code{\LinkA{deGenes2by2Ttest}{deGenes2by2Ttest}},
\code{\LinkA{deGenes2by2Wilcox}{deGenes2by2Wilcox}} and \code{\LinkA{deGenes2by2BootT}{deGenes2by2BootT}}
for analysis between two biological sample types, or function
\code{\LinkA{deGenesANOVA}{deGenesANOVA}}, for analysis between more than two sample
types using ANOVA models.
\end{Description}
\begin{Details}\relax
Objects of this class are produced by calling the functions \code{\LinkA{deGenes2by2Ttest}{deGenes2by2Ttest}},
\code{\LinkA{deGenes2by2Wilcox}{deGenes2by2Wilcox}} and \code{\LinkA{deGenes2by2BootT}{deGenes2by2BootT}}
over an object of class \code{\LinkA{maiges}{maiges}} or by calling the
function \code{\LinkA{deGenesANOVA}{deGenesANOVA}} over an object of class
\code{\LinkA{maigesANOVA}{maigesANOVA}} fitting an ANOVA model to the microarray dataset.
\end{Details}
\begin{Section}{Slots}
\describe{
\item[\code{GeneInfo}:] data frame containing the information
regarding the genes from the dataset.
\item[\code{SampleInfo}:] data frame similar to the \code{GeneInfo}
above, but containing information about the biological sample
types used in the analysis.
\item[\code{fold}:] numerical matrix containing the fold values
(mean difference between the sample types) when two sample types
were compared. Each matrix column gives one specific test.
\item[\code{stat}:] numerical matrix giving the statistic of the
tests that were done. Each column represents on test.
\item[\code{p.value}:] numerical matrix giving the p-values of the
statistical tests. Again, each column represents different tests.
\item[\code{factors}:] character string giving the biological factors
used in ANOVA model (when ANOVA models were used).
\item[\code{test}:] character string describing the test done.
\item[\code{Date}:] character string giving date and time that the
object were created.
\item[\code{V.info}:] list containg three characters. The first one is
a string containing the R version used when the object was
created. The second is a char vector with base packages and the
last one is another char vector with additional packages and
version numbers.
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[plot] \code{signature(x = 'maigesDE')}: plot method for
\code{\LinkA{maigesDE}{maigesDE}} class. Display volcano plots.
\item[print] \code{signature(x = 'maigesDE')}: print method for
\code{\LinkA{maigesDE}{maigesDE}} class.
\item[show] \code{signature(x = 'maigesDE')}: show method for
\code{\LinkA{maigesDE}{maigesDE}} class.
\item[summary] \code{signature(x = 'maigesDE')}: summary method for
\code{\LinkA{maigesDE}{maigesDE}} 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}}.
\end{SeeAlso}

