\HeaderA{arrayQualityMetrics}{Quality metrics on microarray experiments}{arrayQualityMetrics}
\aliasA{arrayQualityMetrics,AffyBatch-method}{arrayQualityMetrics}{arrayQualityMetrics,AffyBatch.Rdash.method}
\aliasA{arrayQualityMetrics,BeadLevelList-method}{arrayQualityMetrics}{arrayQualityMetrics,BeadLevelList.Rdash.method}
\aliasA{arrayQualityMetrics,ExpressionSet-method}{arrayQualityMetrics}{arrayQualityMetrics,ExpressionSet.Rdash.method}
\aliasA{arrayQualityMetrics,NChannelSet-method}{arrayQualityMetrics}{arrayQualityMetrics,NChannelSet.Rdash.method}
\aliasA{arrayQualityMetrics-methods}{arrayQualityMetrics}{arrayQualityMetrics.Rdash.methods}
\keyword{hplot}{arrayQualityMetrics}
\begin{Description}\relax
\code{arrayQualityMetrics} performs quality metrics on
\code{\LinkA{ExpressionSet}{ExpressionSet}},
\code{\LinkA{AffyBatch}{AffyBatch}} or
\code{\LinkA{BeadLevelList}{BeadLevelList}} or
\code{\LinkA{NChannelSet}{NChannelSet}} containing
microarray data from any platforms, one or two channels. The results,
presented in a HTML report, are designated to allow the user
to rapidly assess the quality of a set of arrays.
\end{Description}
\begin{Usage}
\begin{verbatim}
## S4 method for signature 'ExpressionSet':
arrayQualityMetrics(expressionset, outdir,
force, do.logtransform, split.plots, intgroup)

arrayQualityMetrics(expressionset,
                    outdir = getwd(),
                    force = FALSE,
                    do.logtransform = FALSE,
                    split.plots = FALSE,
                    intgroup = "Covariate")

## S4 method for signature 'AffyBatch':
arrayQualityMetrics(expressionset, outdir, force,
do.logtransform, split.plots, intgroup)
## S4 method for signature 'NChannelSet':
arrayQualityMetrics(expressionset, outdir, force, do.logtransform, split.plots, intgroup)
## S4 method for signature 'BeadLevelList':
arrayQualityMetrics(expressionset, outdir,
force, do.logtransform, split.plots, intgroup)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{expressionset}] is an object of
class \code{\LinkA{ExpressionSet}{ExpressionSet}},
\code{\LinkA{AffyBatch}{AffyBatch}} or
\code{\LinkA{BeadLevelList}{BeadLevelList}} or
\code{\LinkA{NChannelSet}{NChannelSet}}.
\item[\code{outdir}] is the name of the directory in which the results are
created. 
\item[\code{force}] if TRUE, \code{outdir} will be overwritten if it
already exists. 
\item[\code{do.logtransform}] If TRUE, the data are log transformed before
the analysis. 
\item[\code{split.plots}] If the number of studied array
is more than 50 it is adviced to define a number of experiments to
represent on the density plots. 
\item[\code{intgroup}] Name of the column of the phenoData to be used to draw
a color side bar next to the heatmap. 
\end{ldescription}
\end{Arguments}
\begin{Value}
A directory \code{outdir} containing a HTML report named QMreport.html and all the PNG and PDF plots is created.
\end{Value}
\begin{Author}\relax
Audrey Kauffmann, Wolfgang Huber. 
Maintainer: <audrey@ebi.ac.uk>
\end{Author}
\begin{Examples}
\begin{ExampleCode}
  ## Not run: 
    library(ALLMLL)
    data(MLL.A)
    arrayQualityMetrics(expressionset = MLL.A,
                        outdir ="MLL",
                        do.logtransform = TRUE,
                        split.plots = 10)
    # "QMreport.html" is a report created in the "MLL" directory
    # on the logarithm expression data of the MLL.A AffyBatch.
    # 10 experiments are represented by density plots.
    
## End(Not run)
\end{ExampleCode}
\end{Examples}

