\HeaderA{nem.cont.preprocess}{Calculate classification probabilities of perturbation data according to control experiments}{nem.cont.preprocess}
\keyword{graphs}{nem.cont.preprocess}
\keyword{models}{nem.cont.preprocess}
\begin{Description}\relax
Calculates probabilities of data to define effects of interventions with respect to wildtype/control measurements
\end{Description}
\begin{Usage}
\begin{verbatim}
nem.cont.preprocess(D,neg.control=NULL,pos.control=NULL,nfold=2, influencefactor=NULL, empPval=.05, verbose=TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{D}] matrix with experiments as columns and effect reporters as rows
\item[\code{neg.control}] either indices of columns in \code{D} or a matrix with the same number of rows as \code{D}
\item[\code{pos.control}] either indices of columns in \code{D} or a matrix with the same number of rows as \code{D}
\item[\code{nfold}] fold-change between neg. and pos. controls for selecting effect reporters. Default: 2
\item[\code{influencefactor}] factor multiplied onto the probabilities, so that all negative control genes are treated as influenced, usually automatically determined
\item[\code{empPval}] empirical p-value cutoff for effects if only one control is available
\item[\code{verbose}] Default: TRUE
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Determines the empirical distributions of the controls and calculates the probabilities of pertubartion data to belong to the control distribution(s).
\end{Details}
\begin{Value}
\begin{ldescription}
\item[\code{dat}] data matrix
\item[\code{pos}] positive controls [in the two-controls setting]
\item[\code{neg}] negative controls [in the two-controls setting]
\item[\code{sel}] effect reporters selected [in the two-controls setting]
\item[\code{prob.influenced}] probability of a reporter to be influenced
\item[\code{influencefactor}] factor multiplied onto the probabilities, so that all negative control genes are treated as influenced
\end{ldescription}
\end{Value}
\begin{Note}\relax
preliminary! will be developed to be more generally applicable
\end{Note}
\begin{Author}\relax
Florian Markowetz \textless{}URL: http://genomics.princeton.edu/\textasciitilde{}florian\textgreater{}
\end{Author}
\begin{References}\relax
Markowetz F, Bloch J, Spang R, Non-transcriptional pathway features reconstructed from secondary effects of RNA interference, Bioinformatics, 2005
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{BoutrosRNAi2002}{BoutrosRNAi2002}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
   data("BoutrosRNAi2002")
   preprocessed <- nem.cont.preprocess(BoutrosRNAiExpression,neg.control=1:4,pos.control=5:8)
\end{ExampleCode}
\end{Examples}

