\HeaderA{QCStats-class}{Class "QCStats"}{QCStats.Rdash.class}
\aliasA{arrayType}{QCStats-class}{arrayType}
\aliasA{arrayType,QCStats-method}{QCStats-class}{arrayType,QCStats.Rdash.method}
\aliasA{arrayType-method}{QCStats-class}{arrayType.Rdash.method}
\aliasA{avbg}{QCStats-class}{avbg}
\aliasA{avbg,QCStats-method}{QCStats-class}{avbg,QCStats.Rdash.method}
\aliasA{avbg-method}{QCStats-class}{avbg.Rdash.method}
\aliasA{maxbg}{QCStats-class}{maxbg}
\aliasA{maxbg,QCStats-method}{QCStats-class}{maxbg,QCStats.Rdash.method}
\aliasA{maxbg-method}{QCStats-class}{maxbg.Rdash.method}
\aliasA{minbg}{QCStats-class}{minbg}
\aliasA{minbg,QCStats-method}{QCStats-class}{minbg,QCStats.Rdash.method}
\aliasA{minbg-method}{QCStats-class}{minbg.Rdash.method}
\aliasA{percent.present}{QCStats-class}{percent.present}
\aliasA{percent.present,QCStats-method}{QCStats-class}{percent.present,QCStats.Rdash.method}
\aliasA{percent.present-method}{QCStats-class}{percent.present.Rdash.method}
\aliasA{plot,QCStats,ANY-method}{QCStats-class}{plot,QCStats,ANY.Rdash.method}
\aliasA{qcProbes}{QCStats-class}{qcProbes}
\aliasA{qcProbes,QCStats-method}{QCStats-class}{qcProbes,QCStats.Rdash.method}
\aliasA{qcProbes-method}{QCStats-class}{qcProbes.Rdash.method}
\aliasA{ratios}{QCStats-class}{ratios}
\aliasA{ratios,QCStats-method}{QCStats-class}{ratios,QCStats.Rdash.method}
\aliasA{ratios-method}{QCStats-class}{ratios.Rdash.method}
\aliasA{sfs}{QCStats-class}{sfs}
\aliasA{sfs,QCStats-method}{QCStats-class}{sfs,QCStats.Rdash.method}
\aliasA{sfs-method}{QCStats-class}{sfs.Rdash.method}
\aliasA{spikeInProbes}{QCStats-class}{spikeInProbes}
\aliasA{spikeInProbes,QCStats-method}{QCStats-class}{spikeInProbes,QCStats.Rdash.method}
\aliasA{spikeInProbes-method}{QCStats-class}{spikeInProbes.Rdash.method}
\aliasA{target}{QCStats-class}{target}
\aliasA{target,QCStats-method}{QCStats-class}{target,QCStats.Rdash.method}
\aliasA{target-method}{QCStats-class}{target.Rdash.method}
\keyword{classes}{QCStats-class}
\begin{Description}\relax
Holds Quality Control data for a set of Affymetrix arrays
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{qc(\LinkA{AffyBatch}{AffyBatch})}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{scale.factors}:] Object of class \code{"numeric"} Scale factors used to scale the chips to the specified target intensity 
\item[\code{target}:] Object of class \code{"numeric"} The target intensity to which the chips were scaled 
\item[\code{percent.present}:] Object of class \code{"numeric"} Number of genes called present 
\item[\code{average.background}:] Object of class \code{"numeric"} The average background for the arrays 
\item[\code{minimum.background}:] Object of class \code{"numeric"} The minimum background for the arrays 
\item[\code{maximum.background}:] Object of class \code{"numeric"} The maximum background for the arrays 
\item[\code{spikes}:] Object of class \code{"list"} spiked in probes (e.g. biob, bioc...) 
\item[\code{qc.probes}:] Object of class \code{"list"} qc probes
(e.g. gapdh 3,5,M,...) 
\item[\code{arrayType}:] The \code{\LinkA{cdfName}{cdfName}} of the
\code{\LinkA{AffyBatch}{AffyBatch}} object used to create the object 
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[avbg] \code{signature(object = "QCStats")}:  average background
\item[maxbg] \code{signature(object = "QCStats")}: maximum background 
\item[minbg] \code{signature(object = "QCStats")}: minimum background 
\item[spikeInProbes] \code{signature(object = "QCStats")}: the spike-in QC probes 
\item[qcProbes] \code{signature(object = "QCStats")}: the gapdh and actin QC probes 
\item[percent.present] \code{signature(object = "QCStats")}: no probesets called present 
\item[plot] \code{signature(x = "QCStats")}: Plot a QCStats object 
\item[sfs] \code{signature(object = "QCStats")}: scale factors 
\item[target] \code{signature(object = "QCStats")}: target scaling 
\item[ratios] \code{signature(object = "QCStats")}: 5'3' and 5'M
ratios for QC Probes 
\item[arrayType] \code{signature(object = "QCStats")}: The type of
array for which this QC stats object was generated 
}
\end{Section}
\begin{Author}\relax
Crispin J Miller
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{qc}{qc}}
\end{SeeAlso}