\name{mae.loessPlot}
\alias{mae.loessPlot}
\title{ A function to generate loess line and fitted plots}

\description{
    A function that generates a loess line and fitted, and optionally
plots for them, for two samples 
}

\usage{
mae.loessPlot(x,y,xName,yName,doPlot=TRUE)
}

\arguments{
    \item{x and y}{are the single sample matrices or data frames}
    \item{xName and yName}{are the sample names}
    \item{doPlot}{=TRUE, if do a plot, else just compute the loess data}
}

\details{
    \code{mae.loessPlot} generate loess line and fitted plots for 
for two samples if doPlot is true. The plots include:
M vs A (loess line), and M vs A (loess fitted) plots.}

\value{A list with components
  \item{AValue}{is c(log10(as.matrix(x)) + log10(as.matrix(y)))/2 }
  \item{MValue}{is c(log2(as.matrix(x)/as.matrix(y))) } 
  \item{dMvsA}{is data.frame(ID=(cbind(x,y)[,1]),AVAL=AValue, MVAL=MValue)} 
  \item{dMvsA.lo }{is loess fit of (MValue ~ AValue)} 
  \item{fitted }{is (MValue-dMvsA.lo$fitted) } 
  \item{sNames}{is c(xName,yName) }

 }

\references{ }
 
\author{ Shyam Sundaram, Peter Lemkin, Greg Thornwal}

\date{ 06/30/2003 }


\examples{
#  ...

}
\keyword{loess }