\HeaderA{meeboQualityPlots}{Qualitative diagnostic plot for general hybridization, specific
to MEEBO set.}{meeboQualityPlots}
\keyword{hplot}{meeboQualityPlots}
\begin{Description}\relax
This function generates diagnostic plots for a qualitative assessment of
slide quality.
\end{Description}
\begin{Usage}
\begin{verbatim}
meeboQualityPlots(mrawObj, headerInfo = "", save = TRUE, dev = "png",
col = NULL, badspotfunction = NULL, controlId = c("ID", "Name"), seqId =
"SeqID", organism = "Mm", 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{seqId}] A "character" string naming the column of the MEEBO
annotation to use to retrieve replicated sequences.
\item[\code{organism}] A "character" string naming the organism genome
printed on the array, either "Mm" or "Hs". By default, organism is
set to "Mm". It is used to retrieve the corresponding Oligo set annotations.
\item[\code{DEBUG}] If 'TRUE', debug statements are printed.
\item[\code{...}] additional arguments
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The right panels of the diagnostic plot contain boxplots of the various
controls in the set, like positive or negative controls, as set in the
marrayRaw of RGlist object. Replicated controls are recognized based on
their MEEBO sequence id.
\end{Details}
\begin{Author}\relax
Agnes Paquet
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{meeboQuality}{meeboQuality}}, \code{\LinkA{gpQuality}{gpQuality}},
\code{\LinkA{maQualityPlots}{maQualityPlots}},\code{\LinkA{MeeboSpotTypes}{MeeboSpotTypes}},
\code{\LinkA{controlCodeMeebo}{controlCodeMeebo}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

if (interactive())
{
require(MEEBOdata)
datadir <- system.file("Meebo", package="MEEBOdata")
mraw <- read.GenePix(path=datadir)
maControls(mraw) <- maGenControls(maGnames(mraw),id="ID",controlcode=controlCodeMeebo)
rownames(maRf(mraw)) <- rownames(maRb(mraw)) <- maGeneTable(mraw)[,"ID"]
rownames(maGf(mraw)) <- rownames(maGb(mraw)) <- maGeneTable(mraw)[,"ID"]
meeboQualityPlots(mraw)
}
\end{ExampleCode}
\end{Examples}

