\HeaderA{PairComp-class}{Class "PairComp" Represents the results of pairwise comparison between two experimental factors}{PairComp.Rdash.class}
\aliasA{calculated.from}{PairComp-class}{calculated.from}
\aliasA{calculated.from,PairComp-method}{PairComp-class}{calculated.from,PairComp.Rdash.method}
\aliasA{calls}{PairComp-class}{calls}
\aliasA{calls,PairComp-method}{PairComp-class}{calls,PairComp.Rdash.method}
\aliasA{fc}{PairComp-class}{fc}
\aliasA{fc,PairComp-method}{PairComp-class}{fc,PairComp.Rdash.method}
\aliasA{group}{PairComp-class}{group}
\aliasA{group,PairComp-method}{PairComp-class}{group,PairComp.Rdash.method}
\aliasA{means}{PairComp-class}{means}
\aliasA{means,PairComp-method}{PairComp-class}{means,PairComp.Rdash.method}
\aliasA{members}{PairComp-class}{members}
\aliasA{members,PairComp-method}{PairComp-class}{members,PairComp.Rdash.method}
\aliasA{pairwise.filter,PairComp-method}{PairComp-class}{pairwise.filter,PairComp.Rdash.method}
\aliasA{pData}{PairComp-class}{pData}
\aliasA{pData,PairComp-method}{PairComp-class}{pData,PairComp.Rdash.method}
\aliasA{plot,PairComp,ANY-method}{PairComp-class}{plot,PairComp,ANY.Rdash.method}
\aliasA{tt}{PairComp-class}{tt}
\aliasA{tt,PairComp-method}{PairComp-class}{tt,PairComp.Rdash.method}
\aliasA{[,PairComp-method}{PairComp-class}{[,PairComp.Rdash.method}
\aliasA{[<-,PairComp-method}{PairComp-class}{[<.Rdash.,PairComp.Rdash.method}
\keyword{classes}{PairComp-class}
\begin{Description}\relax
Holds fold-change, ttest p-score and detection p-value calls(if used) between a pair of experimental factors.
\end{Description}
\begin{Section}{Slots}
\describe{
\item[\code{means}:] Object of class \code{"matrix"} Mean values for each of the experimental factors. 
\item[\code{fc}:] Object of class \code{"numeric"} Fold change between the means 
\item[\code{tt}:] Object of class \code{"numeric"} P-score between the factors 
\item[\code{calls}:] Object of class \code{"matrix"} Detection p-values for each probeset on each array 
\item[\code{group}:] Object of class \code{"character"} The name of the factor that was compared 
\item[\code{members}:] Object of class \code{"character"} A list containing the two levels compared between 
\item[\code{pData}:] Object of class \code{"pData"} The phenoData for the members that were compared 
\item[\code{calculated.from}:] Object of class \code{"exprSet"} The original expression set that was being compared 
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[[] \code{signature(x = "PairComp")}: get the values for the specified gene(s) 
\item[[<-] \code{signature(x = "PairComp")}: not supported. 
\item[calls] \code{signature(object = "PairComp")}: the detection.p.values 
\item[fc] \code{signature(object = "PairComp")}: the fold-changes 
\item[group] \code{signature(object = "PairComp")}: the name of the group that was compared 
\item[means] \code{signature(object = "PairComp")}: the means of the two experimental factors that were compared
\item[members] \code{signature(object = "PairComp")}: the members of that group that were compared 
\item[pairwise.filter] \code{signature(object = "PairComp")}: Take a \code{PairComp} object and filter it to yield probesets that pass the specified criteria 
\item[tt] \code{signature(object = "PairComp")}: the results of a ttest between groups 
\item[pData] \code{signature(object = "pData")}: The phenoData from the members that were compared
\item[calculated.from] \code{signature(object = "exprSet")}: The original expression set 
}
\end{Section}
\begin{Author}\relax
Crispin Miller
\end{Author}
\begin{SeeAlso}\relax
\end{SeeAlso}