\HeaderA{qc}{Generate QC stats from an AffyBatch object}{qc}
\aliasA{qc,AffyBatch-method}{qc}{qc,AffyBatch.Rdash.method}
\keyword{misc}{qc}
\begin{Description}\relax
Generate QC metrix for Affymetrix data.
\end{Description}
\begin{Usage}
\begin{verbatim}
qc(unnormalised, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{unnormalised}] An AffyBatch object with nowt done to it 
\item[\code{...}] Any other parameters 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Affymetrix recommend a series of QC metrics that should be used to
check that arrays have hybridised correctly and that sample quality is
acceptable. These are discussed in the document 'QC and Affymetrix
data' accompanying this package, and on the web at
http://bioinformatics.picr.man.ac.uk. They are described in detail in
the 'Expression Analysis Fundamentals' manual available from
Affymetrix.

Before using this function you are strongly encouraged to read the 'QC
and Affymetrix data' document, which contains detailed examples.

This function takes an \code{\LinkA{AffyBatch}{AffyBatch}} object and generates a \code{\LinkA{QCStats}{QCStats}}
object containing a set of QC metrics. See \code{\LinkA{qc.affy}{qc.affy}} for more details.
\end{Details}
\begin{Author}\relax
Crispin J Miller
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{qc.affy}{qc.affy}}
\code{\LinkA{setQCEnvironment}{setQCEnvironment}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  ## Not run: 
    qcs <- qc(eset,eset.mas)
  
## End(Not run)
  data(qcs)
  ratios(qcs)
  avbg(qcs)
  maxbg(qcs)
  minbg(qcs)
  spikeInProbes(qcs)
  qcProbes(qcs)
  percent.present(qcs)
  plot(qcs)
  sfs(qcs)
  target(qcs)
  ratios(qcs)
\end{ExampleCode}
\end{Examples}