\name{calculatePosteriorAvg}
 \alias{calculatePosteriorAvg}
 \title{Calculate the posterior average for indicators of concordant and
   discordant differential expression}
 
 \description{
   
   This function calculates the posterior average for indicators of concordant and
   discordant differential expression from the saved log files. See details.  
   
 }
 
 \usage{
 calculatePosteriorAvg(object, NCONC=2, NDIFF=1, burnin=0)
 }
 
 \arguments{
   \item{object}{ Object of class \code{XdeMcmc}}
   \item{NCONC}{Integer: number of studies for which the gene must be
     differentially expressed (in the same direction) to be classified as
   concordant differential expression}
   \item{NDIFF}{Integer: number of studies for which a gene must be
     up- or down-regulated to be classified as differentially expressed.
     It is the union of concordant and discordant differential
     expression.}
   \item{burnin}{Integer: number of MCMC iterations for the burnin. Posterior means
   are computed from the MCMC samples following burnin.}
 }
 \details{
 
  For each iteration,
 
 1.  calculate the sign of delta * Delta
  
 2.  For each gene, compute the number of positive signs (P) and the
 number of negative signs (N) (a G x 2 matrix, where G is the number of
 genes in common across all studies).  P + N is <= S, where S is the
 number of studies.
 
 3.  for a given gene, the discordant indicator is simply when P * N
 is nonzero.
 
 4.  The concordant indicator requires P * N = 0 AND P + N >=
 NCONC, where NCONC is specified by the user.
 
 5.  differential expression is simply   | P | + | N |  >= NDIFF.  By
 default, NDIFF is 1 but can be user-specified.
 
 The posterior average is then computed from the mean over all MCMC iterations.
 
 }
 
 \value{
   
   A G x 3 matrix.
   
 }
 
 \author{RS}
 \seealso{\code{\link{posteriorAvg}}}
 \keyword{manip}