\HeaderA{CountPlot}{Plots for Meta-analysis of gene expression data.}{CountPlot}
\aliasA{IDRplot}{CountPlot}{IDRplot}
\begin{Description}\relax
Plots for meta-analysis
\end{Description}
\begin{Usage}
\begin{verbatim}
IDRplot(m,CombineExp=1:(length(grep("zSco_Ex",colnames(m)))),colPos="black",colNeg="red",pchPos="*",pchNeg="*",type="b",ylab="IDR",xlab="z threshold",...)
CountPlot(kkk,cols,Score=c("FDR","zSco"),kindof=c("two.sided","pos","neg"),type="b",pch="*",ylab="Number of genes",xlab="FDR threshold",CombineExp=1:((ncol(m)-6)/2-1) ,...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{m}] result matrix of the function \code{zScores}
\item[\code{type}] plot parameter
\item[\code{ylab}] plot parameter
\item[\code{xlab}] plot parameter
\item[\code{pch}] plot parameter
\item[\code{colPos}] color for positive z scores
\item[\code{colNeg}] color for negative z scores
\item[\code{pchPos}] symbol for positive z scores
\item[\code{pchNeg}] symbol for negative z scores
\item[\code{CombineExp}] vector of integer- which experiments should be combined-default:all experiments
\item[\code{kkk}] result object of function zScoreFDR
\item[\code{cols}] vector of cols, one for each experiment, and one for the combination
\item[\code{Score}] should the FDR or the zScore be plotted
\item[\code{kindof}] "pos", "neg" or "two.sided"
\item[\code{...}] additional plot parameter
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
IDRplot produces a plot described in Choi et al.
\end{Details}
\begin{Value}
\end{Value}
\begin{Author}\relax
M.Ruschhaupt
\end{Author}
\begin{References}\relax
Choi et al, Combining multiple microarray studies and
modeling interstudy variation. Bioinformatics, 2003, i84-i90.
\end{References}
\begin{Examples}
\begin{ExampleCode}\end{ExampleCode}
\end{Examples}

