\HeaderA{globalQuality}{Quality measures for general hybridization.}{globalQuality}
\keyword{programming}{globalQuality}
\begin{Description}\relax
This function provides Quality Control measures for GenePix, Spot and
Agilent format files. It is used to create a table of measures to be used as
reference in gpQuality, spotQuality or agQuality.
\end{Description}
\begin{Usage}
\begin{verbatim}
globalQuality(fnames = NULL, path = ".", organism = c("Mm", "Hs"),
output = FALSE, resdir = ".", DEBUG = FALSE, inputsource = "readGPR",...)
\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{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{output}] Logical. If 'TRUE', the 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{DEBUG}] If 'TRUE', debug statements are printed.
\item[\code{inputsource}] A "character" string providing the name of the function to
use to read the input files. It should be inputsource = "readGPR"
for GenePix format files, inputsource = "readSpot" for Spot files, or
inputsource = "readAgilent" for Agilent format. By default,
'inputsource' is set to "readGPR".
\item[\code{...}] additional arguments
\end{ldescription}
\end{Arguments}
\begin{Value}
A matrix of Quality Control measures, each column representing a
different input slide.
\end{Value}
\begin{Author}\relax
Agnes Paquet
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{gpQuality}{gpQuality}}, \code{\LinkA{slideQuality}{slideQuality}},
\code{\LinkA{MmReferenceDB}{MmReferenceDB}}, \code{\LinkA{readGPR}{readGPR}},
\code{\LinkA{readSpot}{readSpot}}, \code{\LinkA{readAgilent}{readAgilent}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
datadir <- system.file("gprQCData", package="arrayQuality")
if (interactive())
reference <- globalQuality(fnames="9Mm137.gpr", path=datadir, organism="Mm")
\end{ExampleCode}
\end{Examples}

