\HeaderA{qc.read.file}{Read a file defining the QC parameters for a specified array and
set up the QC Environment}{qc.read.file}
\keyword{misc}{qc.read.file}
\begin{Description}\relax
Affymetrix define a series of QC parameters for their arrays. Many of
these rely on specific probeset that differ between arrays and are
used to calculate things like 3'/5' ratios. See \code{\LinkA{qc.affy}{qc.affy}}
for more details. This is usually done by a call to
\code{\LinkA{setQCEnvironment}{setQCEnvironment}}; the function described here is the one
that does the actual loading of the
configuration file.  See the package vignette for details of the config
file's syntax.
\end{Description}
\begin{Usage}
\begin{verbatim}
  qc.read.file(fn)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{fn}] full path and name of the file to load 
\end{ldescription}
\end{Arguments}
\begin{Value}
none.
\end{Value}
\begin{Note}\relax
\end{Note}
\begin{Author}\relax
Crispin J Miller
\end{Author}
\begin{References}\relax
http://bioinformatics.picr.man.ac.uk/
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{setQCEnvironment}{setQCEnvironment}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  fn <- system.file("extdata","hgu133plus2cdf.qcdef",package="simpleaffy")
  qc.read.file(fn)
  qc.get.spikes()
  qc.get.probes()
  qc.get.ratios()
\end{ExampleCode}
\end{Examples}