\HeaderA{setQCEnvironment}{Establish the appropriate QC environment for the specified array}{setQCEnvironment}
\keyword{misc}{setQCEnvironment}
\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{qc.affy}
for more details. These functions are used to set up the appropriate
QC environment for the specified array. This is done by loading a
configuration file, either from the packages data directory, or from
the specified path. See the package vignette for details of the config
file's syntax.
\end{Description}
\begin{Usage}
\begin{verbatim}
 setQCEnvironment(array,path=NULL)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{array}] This should be the 'clean' cdf name of the array as generated by
\code{\LinkA{cleancdfname}{cleancdfname}} in the affy package.
\item[\code{path}] Path to the file. By default, checks the package's own
data directory - only needed if a defininition file is being
specified manually, as described in the vignette.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The usual way to get the 'clean' cdfname is as follows:
\code{cleancdfname(cdfName(eset))}, where \code{eset} is an
\code{\LinkA{AffyBatch}{AffyBatch}} object.
\end{Details}
\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{qc}{qc}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  setQCEnvironment("hgu133plus2cdf")
  setQCEnvironment(cleancdfname("HG-U133_Plus_2"))

\end{ExampleCode}
\end{Examples}