\HeaderA{qualityDiagnostics}{Generates quality diagnostic plots}{qualityDiagnostics}
\keyword{hplot}{qualityDiagnostics}
\begin{Description}\relax
Several quality diagnostic plots are generated.
The distributions of the (normalised) intensities,
as well as overall similarities between hybridisations and
several other quality parameters are graphically visualised
(cf. function \code{\LinkA{qualityParameters}{qualityParameters}}).
\end{Description}
\begin{Usage}
\begin{verbatim}qualityDiagnostics(arrayDataObject, exprSetRGObject, qualityParametersList, groupingColumn, slideNameColumn, savePath=".", completeOutput=FALSE, verbose=TRUE, plotOutput="pdf")\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{arrayDataObject}] \code{\LinkA{arrayData-class}{arrayData.Rdash.class}};
required; default: missing
\item[\code{exprSetRGObject}] \code{\LinkA{exprSetRG-class}{exprSetRG.Rdash.class}};
required, default: missing
\item[\code{qualityParametersList}] the return value of
\code{\LinkA{qualityParameters}{qualityParameters}}
required; default: missing
\item[\code{groupingColumn}] character string; optional; default: missing;
specifies a column of
\code{pDataSlide(exprSetRGObject)} which is
used to indicate the hybridisation groups
in the clustered similarity plots.
\item[\code{slideNameColumn}] character string; optional; default: missing;
specifies a column of
\code{pDataSlide(exprSetRGObject)}.
\item[\code{savePath}] character string; required; default: "."
\item[\code{completeOutput}] required; default: \code{FALSE}
\item[\code{verbose}] logical; required; default: \code{TRUE}
\item[\code{plotOutput}] character string specifying the output type;
either "screen", "pdf" or "win.metafile"; default: "pdf"
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\end{Details}
\begin{Value}
The function is called for its side effect.
\end{Value}
\begin{Author}\relax
Andreas Buness <a.buness@dkfz.de>
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{qualityParameters}{qualityParameters}},
\code{\LinkA{exprSetRG-class}{exprSetRG.Rdash.class}},
\code{\LinkA{arrayData-class}{arrayData.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
        \end{ExampleCode}
\end{Examples}

