\HeaderA{read.cdf.env}{Creating an CDF environment using teh Fusion SDK}{read.cdf.env}
\keyword{file}{read.cdf.env}
\begin{Description}\relax
This function parses a CDF file and creates a corresponding CDF
environment using the Afymetrix Fusion SDK.
\end{Description}
\begin{Usage}
\begin{verbatim}
read.cdf.env(fname, complementary.logic = TRUE, verbose = 0)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{fname}] name of the CDF file.
\item[\code{complementary.logic}] is a sanity check performed where we
require that the mm match for a pm probe should be exactly the
complementary of the pm probe. This should be the case for all cdf
files except very special custom files (and SNP chip files).
\item[\code{verbose}] how verbose do we want to be? 0 means no output, higher
numbers is more verbose.
\end{ldescription}
\end{Arguments}
\begin{Value}
A cdf envirornment, for details see the link below.
\end{Value}
\begin{Note}\relax
~~further notes~~
\end{Note}
\begin{Author}\relax
James Bullard, \email{bullard@stat.berkeley.edu} and Kasper
Daniel Hansen, \email{khansen@stat.berkeley.edu}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{make.cdf.env}{make.cdf.env}} from \pkg{makecdfenv}
for the default approach to creating cdf environments as well as
\code{\LinkA{affxparserInfo}{affxparserInfo}} for general information about the Fusion
SDK.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Not run: 
read.cdf.env("test.CDF")
## End(Not run)
\end{ExampleCode}
\end{Examples}

