\name{agQuality}
\alias{agQuality}
\alias{agcontrolCode}
\title{Diagnostic plots and comparative boxplots for general
  hybridization, Agilent format}
\description{
  This component provides qualitative diagnostic plots and quantitative
  measures for assessing general hybridization quality. All results are
  displayed in a HTML report. Agilent format only.}
\usage{
agQuality(fnames = NULL, path = ".", organism = c("Mm", "Hs"),
compBoxplot = TRUE, reference = NULL, controlMatrix = agcontrolCode,
controlId = c("ProbeName"), output = FALSE, resdir = ".", dev= "png", DEBUG = FALSE,...)
}
\arguments{ 
  \item{fnames}{A "character" string naming the input files.}
  \item{path}{A "character" string representing the data directory. By
    default this is set to the current working directory (".").}
  \item{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{compBoxplot}{Logical. If set to 'FALSE', only qualitative
    diagnostic plots will be plotted. agQuality ouput will be limited to
    a diagnostic plot by file and a marrayRaw object.}
  \item{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{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. By
    default, is it set to be agcontrolCode.}
  \item{controlId}{Character string. Name of the column of the file used
    to define controls.}
  \item{output}{Logical. If 'TRUE', normalized M values corresponding to
    the input Agilent files and quality measures are printed to a file.}
  \item{resdir}{A "character" string representing the directory where
    the results will be saved. By default, this is set to the current
    working directory (".").}
  \item{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{DEBUG}{If 'TRUE', debug statements are printed.}
  \item{\dots}{Additional arguments.}
}
\details{
  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.
}
\value{
  A list of 2 elements:
  \item{mraw}{A marrayRaw object created from the input files.}
  \item{quality}{A matrix containing Quality Control measures for all slides.}
}
\author{Agnes Paquet}
\seealso{
  \code{\link{globalQuality}}, \code{\link{qualBoxplot}},
  \code{\link{readAgilent}}
}
\examples{ example}
\keyword{hplot}