\HeaderA{affxparserInfo}{Overview of the Affxparser package.}{affxparserInfo}
\keyword{file}{affxparserInfo}
\begin{Description}\relax
The package implements an interface to the Fusion SDK from
Affymetrix.com.
\end{Description}
\begin{Usage}
\begin{verbatim}
  affxparserInfo(fusion.license = FALSE, file.changes = FALSE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{fusion.license}] display the license of the Fusion SDK (this will
happen in a browser).
\item[\code{file.changes}] display the changes made to the Fusion SDK.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This package implements an interface to the Fusion SDK from
Affymetrix.com. This SDK (software development kit) is an open source
library used for parsing the various files formats used by the
Affymetrix platform.

The intention is to provide interfaces to most if not all file formats
which may be parsed using Fusion.

The SDK supports parsing of all the different versions of a specific
fileformat. This means that ascii, binary as well as the new binary
format (codename Calvin) used by Affymetrix is supported through a
single API. We also expect any future changes to the file formats to
be reflected in the SDK, and subsequently in this package.

However, as the current Fusion SDK does not support compressed files,
neither does \pkg{affxparser}. This is in contrast to some of the
existing code in \pkg{affy} and relatives (see below for links).

In general we aim to provide functions returning all information in
the respective files. Currently it seems that future Affymetrix chip
designs may consists of so many features that returning all
information will lead to an unnecessary overhead on the case a user
only wants access to a subset. We have tried to make this possible.

For older file, certain entries in the files have been removed from
newer specifications, and the SDK does not provide utilities for
reading these entries. This includes eg. the FEAT column of CDF files.

Currently the package as well as the Fusion SDK is in beta stage. Bugs
may be related to either codebase. We are very interested in users
being unable to compile/parse files using this library - this includes
users with custom chip designs.

In addition, since we aim to return all information stored in the
file (and accessible using the Fusion SDK) we would like reports from
users being unable to do that.

The efficiency of the underlying code may vary with the version of the
file being parsed. For example, we currently report the number of
outliers present in a CEL file. In order to obtain this information
from text based CEL files (version 2), the entire file needs to be
read into memory. With version 3 of the file format, this information
is stored in the header.

With the introduction of the Fusion SDK (and the next version of their
file formats) Affymetrix has made it possible to use multibyte
character sets. This implies that character information may be
inaccesible if the compiler used to compile the c++ code does not
support multibyte character sets (specifically we require that the R
installation has defined the macro \code{SUPPORT\_MCBS} in the
\code{Rconfig.h} header file).

The \code{affxparserInfo} function returns relevant information
regarding the version of the Fusion SDK (and possibly more). It simply
echoes the README file in the package directory.
\end{Details}
\begin{Author}\relax
James bullard, \email{bullard@stat.berkeley.edu} and
Kasper Daniel Hansen, \email{khansen@stat.berkeley.edu}
\end{Author}
\begin{References}\relax
\url{http://www.affymetrix.com}, particular the support and
developer parts of the website.
\end{References}
\begin{SeeAlso}\relax
Existing functions for parsing Affymetrix files may be found in
\pkg{affy}, \pkg{oligo}, \pkg{makecdfenv} and
\pkg{makePlatformDesign}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  affxparserInfo()
\end{ExampleCode}
\end{Examples}

