\HeaderA{spotQuality}{Diagnostic plots and comparative boxplots for general
hybridization, Spot format}{spotQuality}
\keyword{hplot}{spotQuality}
\begin{Description}\relax
This component provides qualitative diagnostic plots and quantitative
measures for assessing general hybridization quality. All results are
displayed in a HTML report. Spot format only.
\end{Description}
\begin{Usage}
\begin{verbatim}

spotQuality(fnames = NULL, path = ".", galfile = NULL, organism = c("Mm", "Hs"),
compBoxplot = TRUE, reference = NULL, controlMatrix = controlCode,
controlId = c("ID"), output = FALSE, resdir = ".", dev= "png", DEBUG = FALSE,...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{fnames}] A "character" string naming the input files.
\item[\code{path}] A "character" string representing the data directory.  By
default this is set to the current working directory (".").
\item[\code{galfile}] A "character" string naming the galfile associated with
the input files. If galfile = NULL, spotQuality will use the first
.gal file available in the working directory.
\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{compBoxplot}] Logical. If set to 'FALSE', only qualitative
diagnostic plots will be plotted. gpQuality ouput will be limited to
a diagnostic plot by gpr file and a marrayRaw object.
\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{controlMatrix}] A character matrix of n by 2 columns. The first
column contains a few regular expression of spotted probe sequences
and the second column contains the corresponding control status.
\item[\code{controlId}] Character string. Name of the column of the gpr
file used to define controls.
\item[\code{output}] Logical. If 'TRUE', normalized M values corresponding to
the input GenePix files and quality measures are printed to a file.
\item[\code{resdir}] A "character" string representing the directory where
the results will be saved. By default, this is set to the current
working directory ("."). 
\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{DEBUG}] If 'TRUE', debug statements are printed.
\item[\code{...}] additional arguments
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
agQuality returns 2 plots for each Agilent files passed as argument. The
first one is a qualitative diagnostic plot, a quick visual way to assess
slide quality. The second one is a comparative boxplot: each quality
control measure is compared to the range obtained for a database of 'good'
slides used as reference. 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} and \code{HsReferenceDB}. All results and quality
scores are gathered in a HTML report. For more details about the QC measures and the plots, please refer to the online manual.
\end{Details}
\begin{Value}
A list of 2 elements:

\begin{ldescription}
\item[\code{mraw}] A marrayRaw object created from the input files.
\item[\code{quality}] A matrix containing Quality Control measures for all slides.
\end{ldescription}
\end{Value}
\begin{Author}\relax
Agnes Paquet
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{globalQuality}{globalQuality}}, \code{\LinkA{qualBoxplot}{qualBoxplot}},
\code{\LinkA{readAgilent}{readAgilent}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
\end{ExampleCode}
\end{Examples}

