\name{plotMA}
\alias{plotMA}
\title{Show MA plots}
\description{
Function which produces an MA plot between two specified arrays.
}
\usage{
plotMA(exprs, array1=1, array2=2, genesToLabel=NULL, labelCol="red", foldLine=2, log=TRUE, labelpch=16, ma.ylim=2, sampleSize=NULL,...)
}
\arguments{
  \item{exprs}{a matrix of expression values}
  \item{array1}{integer specifying the first array to plot}
  \item{array2}{integer specifying the second array to plot}
  \item{genesToLabel}{vector of genes to highlight on the plot. 
     These must match the rownames of \code{exprs}.}
  \item{labelCol}{plotting colours for highlighted genes}
  \item{foldLine}{a numeric value defining where to draw horizontal fold-change lines on the plot}
  \item{log}{if TRUE the data will be log-transformed before plotting}
  \item{labelpch}{plotting characters for highlighted genes}
  \item{ma.ylim}{numeric value specifying the range of the plot (from -ma.ylim to ma.ylim)}
  \item{sampleSize}{The number of genes to plot.  Default is NULL, which plots every gene.}
  \item{\dots}{other graphical parameters to plot that can be specified}
}
\details{

The log2 difference in intensity (M-value, log-ratio) are plotted against the log2 average intensity (A-value) for each probe for the two arrays selected.

  As a result of both having identical function names this function can conflict with the \code{\link[limma:plotma]{plotMA}} method in 'limma'.  If both packages are loaded, the function from whichever package was loaded last takes precedence.  If the 'beadarray' plotMA() function is masking that from 'limma', one can directly call the 'limma' method using the command "limma::plotMA()".  Alternatively, one can detach the 'beadarray' package using "detach(package:beadarray)".  Similar techniques can be used if 'limma' is masking the 'beadarray' method.
}
\value{
A smoothed MA scatter plot is displayed on the current graphical device.
}

\author{Mark Dunning}

\examples{
data(BSData)

plotMA(exprs(BSData), array1=1, array2=2)
}
\keyword{hplot}