\name{poe.mcmc}
\alias{poe.mcmc}
\title{Probability of Expression (POE)}
\description{
  Differential expression using latent categories of up/down regulation. 
  Three component normal-uniform mixture model under Bayesian hierarchical analysis.
  This is a C implementation of poe.fit function of POE package (MCMC). R portion of source code
  was directly adapted from POE; poe.one.iteration function was re-written in C.
  Some of the optional arguments available in poe.fit are suppressed here, and you cannot save the chain of
  samples drawn for numerical integration.
}
\usage{
  poe.mcmc(AA, NN = NULL, id = NULL, M = 2000, kap.min=3.0,
      logdata=FALSE, stepsize=0.5, 
      centersample = FALSE, centergene = FALSE, generatestarts = TRUE, start.method = 1,
      startobject = R0, collapse.to.two = FALSE, burnin=200,
      collapse.window=50, converge.threshold=0.01,
      PR = list(alpha.mm = 0, alpha.sd = 100, mu.mm = 0, mu.sd = 100,
          pipos.mm = 0, pipos.sd = 100, pineg.mm = 0, pineg.sd = 100,
          kap.pri.rate = 1, tausqinv.aa = 1, tausqinv.bb = 0.1))
  # poe.mcmc(AA = chen, NN = 1 - chen.spl$metastasis, M=2000)
}
\arguments{
  \item{AA}{Matrix or \code{exprs} from an \code{ExpressionSet} object.}
  \item{NN}{Phenotypic label of arrays. If provided, all genes from arrays with label 1 are
            forced e=0 in all iterations. A gene with e=0 is involved in sampling of 
            mu and alpha. For arrays with label 0, e is assumed to be unknown, thus sampled
            differently at every iteration. If this slot is left NULL, all arrays will be marked 0, 
            so that the effect of the latter above applies to all arrays.}        
  \item{M}{Number of MCMC iterations after burn-in.}
}
\value{
  \item{poe }{Probability of over/under expression. Transformed gene expression on a fixed 
scale of [-1,1].}
  \item{Other values }{Posterior median estimates of parameters. Please refer to POE package for details.}
}
\references{G. Parmigiani et al, JRSS, 64:717-736, 2002 or URL: http://astor.som.jhmi.edu/poe/}
\author{Debashis Ghosh <ghoshd@umich.edu>, Hyungwon Choi <hwchoi@umich.edu>}
\examples{
  # poe.mat <- poe.mcmc(AA=exprmat, NN=clvec, M=10000)
  # One can also provide different hyperparameter values. 
}
\keyword{internal}