\HeaderA{topRankSummary}{Return or plots analysis result for top ranking or selected probe sets}{topRankSummary}
\aliasA{plotSummaryLog2FC}{topRankSummary}{plotSummaryLog2FC}
\aliasA{plotSummaryT}{topRankSummary}{plotSummaryT}
\keyword{univar}{topRankSummary}
\keyword{manip}{topRankSummary}
\begin{Description}\relax
Returns (or plots) t-statistic and/or log2FC for each probe and median for each probe set.
P
\end{Description}
\begin{Usage}
\begin{verbatim}

plotSummaryLog2FC(model,nGenes=50,genesOfRank=1:nGenes,genes=NULL)
plotSummaryT(model,nGenes=50,genesOfRank=1:nGenes,genes=NULL)
topRankSummary(model,nGenes=50,genesOfRank=1:nGenes,genes=NULL)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{model}] On object obtained from the function plw.
\item[\code{nGenes}] Gives summary for the nGenes top ranking genes
\item[\code{genesOfRank}] Gives summary for genes ranked genesOfRank
\item[\code{genes}] Gives summary for specific genes.
\end{ldescription}
\end{Arguments}
\begin{Author}\relax
Magnus \eqn{\mbox{\AA}}{A}strand
\end{Author}
\begin{SeeAlso}\relax
plw
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

# ------------------------------------------
# Example using the result of the analysis of
# the 6 arrays in the AffySpikeU95Subset data set

# Loading the data
data(AffySpikeU95Subset)

# Defining design and contrast matrix
group<-factor(rep(1:2,each=3))
design<-model.matrix(~group-1)
contrast<-matrix(c(1,-1),1,2)

# Analyzing using plw
model1<-plw(AffySpikeU95Subset,design=design,contrast=contrast,
            epsilon=0.01)

## Selecting top genes
topRankSummary(model1,nGenes=10)

## Plotting t-statistics and log2FC for top genes
par(mfrow=c(1,2))
plotSummaryT(model1,nGenes=20)
plotSummaryLog2FC(model1,nGenes=20)
\end{ExampleCode}
\end{Examples}

