\HeaderA{qualBoxplot}{Comparative boxplot for general hybridization Quality Control}{qualBoxplot}
\keyword{hplot}{qualBoxplot}
\begin{Description}\relax
This functions allows you to graphically compare your slide
quality measures to results obtained for a database of 'good quality'
slides.
\end{Description}
\begin{Usage}
\begin{verbatim}
qualBoxplot(arrayQuality = NULL, reference = NULL, organism = c("Mm", "Hs"), DEBUG=FALSE,...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{arrayQuality}] Matrix of quality results from \code{slideQuality}
or \code{globalQuality}.
\item[\code{reference}] A matrix resulting from globalQuality, to be used as
reference table to compare slides. If 'NULL', the default table
corresponding to "organism" will be used. See details for more information.
\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 reference
tables.
\item[\code{DEBUG}] If 'TRUE', debug statements are printed.
\item[\code{...}] additional arguments
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
You can use your own set of references created
using \code{globalQuality} passed
in the arguments "reference", or use
the reference QC values stored in the datasets \code{MmReferenceDB}.
\end{Details}
\begin{Value}
Returns a score vector containing, for each column in "arrayQuality",
the number of quality measures below the range of "reference". The
last element of the score vector is the total number of quality
measures tested.
\end{Value}
\begin{Author}\relax
Agnes Paquet
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{globalQuality}{globalQuality}}, \code{\LinkA{gpQuality}{gpQuality}},
\code{\LinkA{spotQuality}{spotQuality}}, \code{\LinkA{agQuality}{agQuality}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
#datadir <- system.file("gprQCData", package="arrayQuality")
#gprData <- readGPR(fnames="9Mm137.gpr", path=datadir)
#arrayQuality <- slideQuality(gprData, organism="Mm")
#qualBoxplot(arrayQuality)
\end{ExampleCode}
\end{Examples}

