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 \name{plotMvsAPairs.matrix}
\alias{plotMvsAPairs.matrix}
\alias{plotMvsAPairs.matrix}


 \title{Plot log-ratios/log-intensities for all unique pairs of data vectors}

 \description{
   Plot log-ratios/log-intensities for all unique pairs of data vectors.
 }

 \usage{\method{plotMvsAPairs}{matrix}(X, Alab="A", Mlab="M", Alim=c(0, 16), Mlim=c(-1, 1) * diff(Alim), pch=".", ..., add=FALSE)}

 \arguments{
  \item{X}{NxK \code{\link[base]{matrix}} where N is the number of observations and
    K is the number of channels.}
  \item{Alab,Mlab}{Labels on the x and y axes.}
  \item{Alim,Mlim}{Plot range on the A and M axes.}
  \item{pch}{Plot symbol used.}
  \item{...}{Additional arguments accepted by \code{\link[graphics]{points}}.}
  \item{add}{If \code{\link[base:logical]{TRUE}}, data points are plotted in the current plot,
    otherwise a new plot is created.}
 }

 \details{
  Log-ratios and log-intensities are calculated for each neighboring pair
  of channels (columns) and plotted. Thus, in total there will be K-1
  data set plotted.

  The colors used for the plotted pairs are 1, 2, and so on. To change
  the colors, use a different color palette.
 }

 \value{
   Returns nothing.
 }

 \author{Henrik Bengtsson (\url{http://www.braju.com/R/})}
\keyword{methods}