\HeaderA{XhybExamples-class}{Class "XhybExamples"}{XhybExamples.Rdash.class}
\aliasA{plotExample,XhybExamples-method}{XhybExamples-class}{plotExample,XhybExamples.Rdash.method}
\keyword{classes}{XhybExamples-class}
\begin{Description}\relax
Class containing information of cross-hybridisation examples
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("XhybExamples", ...)}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{X}:] Object of class \code{"character"} 
contains the ID of probe set X
\item[\code{Y}:] Object of class \code{"character"} 
contains the ID of probe set Y
\item[\code{IVX}:] Object of class \code{"numeric"} 
contains the expression intensities of X in the Tissue dataset 
\item[\code{IVY}:] Object of class \code{"numeric"} 
contains the expression intensities of Y in the Tissue dataset  
\item[\code{IVXi}:] Object of class \code{"matrix"} 
contains the expression intensities of X's reporters in the Tissue dataset 
\item[\code{ai}:] Object of class \code{"numeric"} 
contains the alignment scores of X's reporters to Y's transcript sequence
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[plotExample] \code{signature(ex = "XhybExamples")}: ... 
}
\end{Section}
\begin{Author}\relax
Tineke Casneuf \email{tine@ebi.ac.uk}
\end{Author}
\begin{References}\relax
Casneuf, Van de Peer and Huber (submitted); 
AtgenExpress data used: Schmid, M., Davison, T. S., Henz, S. R., Pape, U. J., Demar, M., Vingron, M. Schoelkopf, B. Weigel, D., and Lohmann, J. (2005) A gene expression map of Arabidopsis development. Nature Genetics, 37, 501-506.
\end{References}
\begin{Examples}
\begin{ExampleCode}
data(ex1)
data(ex2)
data(ex3)
plotExample(ex1)
plotExample(ex2)
plotExample(ex3)
\end{ExampleCode}
\end{Examples}

