\name{MVAplotMEDctrl}
\alias{MVAplotMEDctrl}
\title{ MVA plot }
\description{
	For each array, the M value is computed for every spot as the difference
        between the spot intensity in the array and the averaged intensity for that feature over the whole
        set of arrays. 
	Every kind of feature is identified with different color (gene, controls, etc ...)
}
\usage{
MVAplotMEDctrl(RGlist, maintitle, channel = NULL)
}
\arguments{
  \item{RGlist}{An RGlist object  }
  \item{maintitle}{ character to indicate the title of the graph }
  \item{channel}{if 'channel=R', then uses the data stored in dd$R, if channel
                is missing or 'channel =G' then the data stored in dd$G is used } 
}
\author{ Pedro Lopez-Romero }
\examples{
        data(dd)
	par(mfrow=c(1,1),ask=TRUE)	
        MVAplotMEDctrl(dd,"MVA example",channel="G")
}
\keyword{documentation}
\keyword{utilities}