\HeaderA{maQualityPlots}{Qualitative diagnostic plot for general hybridization}{maQualityPlots}
\keyword{hplot}{maQualityPlots}
\begin{Description}\relax
This function generates diagnostic plots for a qualitative assessment of
slide quality.
\end{Description}
\begin{Usage}
\begin{verbatim}
maQualityPlots(mrawObj, headerInfo = "", save = TRUE, dev = "png", col=NULL,
badspotfunction=NULL, controlId = c("ID", "Name"), DEBUG = FALSE, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{mrawObj}] \code{marrayRaw}  or \code{RGList} object representing
the slides to be tested.
\item[\code{headerInfo}] Text to be used as header in the diagnostic plot.
\item[\code{save}] Logical. If 'TRUE', the plot is saved to a file.
\item[\code{dev}] A "character" string naming the graphics device. This will
take arguments "png", "jpeg" and "ps" only. By default, dev is set
to "png".
\item[\code{col}] Vector of colors to use to describe different
categories of spots.
\item[\code{badspotfunction}] Function to use for bad spots on the array.
\item[\code{controlId}] Character string. Name of the column of the gpr
file used to define controls (or provides the name of the probes).
\item[\code{DEBUG}] If 'TRUE', debug statements are printed.
\item[\code{...}] additional arguments
\end{ldescription}
\end{Arguments}
\begin{Author}\relax
Jean Yang
\end{Author}
\begin{Examples}
\begin{ExampleCode}
# Example uses swirl dataset...

\end{ExampleCode}
\end{Examples}

