\HeaderA{plotMA3by2}{Write MA-Plots to Files}{plotMA3by2}
\keyword{hplot}{plotMA3by2}
\begin{Description}\relax
Write MA-plots to files in PNG format, six plots to a file in a 3 by 2 grid arrangement.
\end{Description}
\begin{Usage}
\begin{verbatim}
plotMA3by2(MA, prefix="MA", path=NULL, main=colnames(MA), zero.weights=FALSE, common.lim=TRUE, device="png", ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{MA}] an \code{MAList} or \code{RGList} object, or any list with components \code{M} containing log-ratios and \code{A} containing average intensities
\item[\code{prefix}] character string giving prefix to attach to file names
\item[\code{path}] character string specifying directory for output files
\item[\code{main}] character vector giving titles for plots
\item[\code{zero.weights}] logical, should points with non-positive weights be plotted
\item[\code{common.lim}] logical, should all plots on a page use the same axis limits
\item[\code{device}] device driver for the plot. Choices are \code{"png"}, \code{"jpeg"}, \code{"pdf"}, \code{"postscript"}.
\item[\code{...}] any other arguments are passed to \code{plotMA}
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function writes a series of graphic files to disk.
Each file contains six MA-plots in three rows and two columns.
The layout is optimized for A4-sized paper.

The graph format can be \code{"png"} or \code{"jpeg"}, which are screen-resolution formats, or \code{"pdf"} or \code{"postscript"}, which are loss-less formats.
\code{"png"} is not available on every R platform.
Note that \code{"pdf"} or \code{"postscript"} may produce very large files.
\end{Details}
\begin{Value}
No value is returned, but one or more files are written to the working directory.
The number of files is determined by the number of columns of \code{MA}.
\end{Value}
\begin{Author}\relax
Gordon Smyth
\end{Author}
\begin{SeeAlso}\relax
An overview of diagnostic functions available in LIMMA is given in \LinkA{09.Diagnostics}{09.Diagnostics}.
\end{SeeAlso}

