\name{plgem.pValue}
\alias{plgem.pValue}
\title{Computation of PLGEM p-values}
\description{
  This function computes p-values for observed PLGEM signal-to-noise ratio (STN)
  values (typically obtained via a call to \code{\link{plgem.obsStn}}) from
  resampled STN values (typically obtained via a call to
  \code{\link{plgem.resampledStn}}).
}
\usage{
  plgem.pValue(observedStn, plgemResampledStn, verbose=FALSE)
}
\arguments{
  \item{observedStn}{\code{list} containing a \code{matrix} of observed
    PLGEM-STN values; output of function \code{\link{plgem.obsStn}}.}
  \item{plgemResampledStn}{\code{list} containing a \code{matrix} of resampled
    PLGEM-STN values; output of function \code{\link{plgem.resampledStn}}.}
  \item{verbose}{\code{logical}; if \code{TRUE}, comments are printed out while
    running.}
}
\details{
  The p-value of each given observed STN value is computed based on the quantile
  that the given value occupies in the corresponding distribution of
  resampled PLGEM-STN values, based on the following relationship:
  \deqn{P=min(2*quantile, 2*(1-quantile))}{%
  p-value = min(2*quantile, 2*(1-quantile))}
}
\value{
  A \code{matrix} with the same \code{\link{dim}}ensions and
  \code{\link{dimnames}} as the input \code{observedStn$PLGEM.STN}, where each
  entry represents the p-value of the corresponding observed PLGEM-STN value.
}
\references{
  Pavelka N, Pelizzola M, Vizzardelli C, Capozzoli M, Splendiani A, Granucci F,
  Ricciardi-Castagnoli P. A power law global error model for the identification
  of differentially expressed genes in microarray data. BMC Bioinformatics. 2004
  Dec 17; 5:203; \url{http://www.biomedcentral.com/1471-2105/5/203}.

  Pavelka N, Fournier ML, Swanson SK, Pelizzola M, Ricciardi-Castagnoli P,
  Florens L, Washburn MP. Statistical similarities between transcriptomics and
  quantitative shotgun proteomics data. Mol Cell Proteomics. 2008 Apr;
  7(4):631-44; \url{http://www.mcponline.org/cgi/content/abstract/7/4/631}.
}
\author{
  Mattia Pelizzola \email{mattia.pelizzola@gmail.com}

  Norman Pavelka \email{normanpavelka@gmail.com}
}
\seealso{
  \code{\link{plgem.fit}}, \code{\link{plgem.obsStn}},
  \code{\link{plgem.resampledStn}}, \code{\link{plgem.deg}},
  \code{\link{run.plgem}}
}
\examples{
  data(LPSeset)
  LPSfit <- plgem.fit(data=LPSeset)
  LPSobsStn <- plgem.obsStn(data=LPSeset, plgemFit=LPSfit)
  head(LPSobsStn[["PLGEM.STN"]])
  set.seed(123)
  LPSresampledStn <- plgem.resampledStn(data=LPSeset, plgemFit=LPSfit)
  LPSpValues <- plgem.pValue(LPSobsStn, LPSresampledStn)
  head(LPSpValues)
}
\keyword{models}