\HeaderA{getProbeDataAffy}{Read a data file describing the probe sequences on an Affymetrix genechip}{getProbeDataAffy}
\keyword{IO}{getProbeDataAffy}
\keyword{utilities}{getProbeDataAffy}
\begin{Description}\relax
Read a data file describing the probe sequences on an Affymetrix genechip
\end{Description}
\begin{Usage}
\begin{verbatim}
getProbeDataAffy(arraytype, datafile, pkgname = NULL, comparewithcdf = TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{arraytype}] Character. Array type (e.g. 'HG-U133A')
\item[\code{datafile}] Character. The filename of the input data file.
If omitted a default name is constructed from \code{arraytype}
(see this function's source code).
\item[\code{pkgname}] Character. Package name. If NULL the name is derived
from \code{arraytype}.
\item[\code{comparewithcdf}] Logical. If TRUE, run a consistency check
against a CDF package of the same name (what used to be Laurent's
"extraparanoia".)
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function serves as an interface between
the (1) representation of array probe information data in the packages
that are generated by \code{\LinkA{makeProbePackage}{makeProbePackage}} and (2) the
vendor- and possibly version-specific way the data are represented
in \code{datafile}.

\code{datafile} is a tabulator-separated file with one row per probe,
and column names \code{'Probe X'}, \code{'Probe Y'},
\code{'Probe Sequence'}, and \code{'Probe.Set.Name'}. See the vignette
for an example.
\end{Details}
\begin{Value}
A list with three components
\begin{ldescription}
\item[\code{dataEnv}] an environment which contains the data frame with the
probe sequences and the other probe data.
\item[\code{symVal}] a named list of symbol value substitutions which can
be used to customize the man pages. See
\code{\LinkA{createPackage}{createPackage}}.
\item[\code{pkgname}] a character with the package name; will be the same
as the function parameter \code{pkgname} if it was specified;
otherwise, the name is constructed from the parameter \code{arraytype}.
\end{ldescription}

normal-bracket36bracket-normal
\end{Value}
\begin{SeeAlso}\relax
makeProbePackage
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  ## Please refer to the vignette
\end{ExampleCode}
\end{Examples}

