\HeaderA{deGenes2by2BootT}{Function to do differential expression analysis, comparing only two
samples}{deGenes2by2BootT}
\keyword{methods}{deGenes2by2BootT}
\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
only two samples by a bootstrap of t statistics method.
\end{Description}
\begin{Usage}
\begin{verbatim}
deGenes2by2BootT(data=NULL, sLabelID=names(data@Slabels)[1], sTypeComp=NULL,
                 doClust=TRUE, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{data}] object of class \code{\LinkA{maiges}{maiges}}.
\item[\code{sLabelID}] character string giving the sample label ID to be used.
\item[\code{sTypeComp}] list with character vectors specifying the two
sample types to be compared.
\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 for functions
\code{\LinkA{t.test}{t.test}}, \code{\LinkA{wilcox.test}{wilcox.test}} or
\code{\LinkA{bootstrapT}{bootstrapT}}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function calculate t statistics and p-values by re-sampling of
the data using the function \code{\LinkA{bootstrapT}{bootstrapT}}.

There is the option to do the t test directly, using the function
\code{\LinkA{deGenes2by2Ttest}{deGenes2by2Ttest}}, or to do the non-parametric Wilcox
test using the function \code{\LinkA{deGenes2by2Wilcox}{deGenes2by2Wilcox}}.
\end{Details}
\begin{Value}
The result of this function 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{bootstrapT}{bootstrapT}}, \code{\LinkA{deGenes2by2Ttest}{deGenes2by2Ttest}} and \code{\LinkA{deGenes2by2Wilcox}{deGenes2by2Wilcox}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Loading the dataset
data(gastro)

## Doing bootstrap from t statistic test fot 'Type' sample label, k=1000
## specifies one thousand bootstraps
gastro.boot = deGenes2by2BootT(gastro.summ, sLabelID="Type", k=1000)
gastro.boot
\end{ExampleCode}
\end{Examples}

