\HeaderA{AffymetrixDataTestFiles-package}{Package AffymetrixDataTestFiles}{AffymetrixDataTestFiles.Rdash.package}
\aliasA{AffymetrixDataTestFiles}{AffymetrixDataTestFiles-package}{AffymetrixDataTestFiles}
\keyword{package}{AffymetrixDataTestFiles-package}
\begin{Description}\relax
This package contains annotation data files and sample
data files of Affymetrix file formats.  The files originate from the
Affymetrix' Fusion SDK distribution.
This package contains only data files.
\end{Description}
\begin{Section}{Requirements}
None.
\end{Section}
\begin{Section}{Installation}
To install this package, see \url{http://www.bioconductor.org/}.
\end{Section}
\begin{Section}{Location of data files}
Data files are located in two different directory tree depending if
they are annotation data files or sample data files.
The roots of these two directory structures are:
\begin{alltt}
     system.file("annotationData", package="AffymetrixDataTestFiles")
     system.file("rawData", package="AffymetrixDataTestFiles")
\end{alltt}
Where applicable, ASCII, XDA, and Calvin files are separated in
different subdirectories for easy access to either type.

Directory structure:
\begin{alltt}
   annotationData/
    chipTypes/
      HG-Focus/
        +-HG-Focus.PSI
        3.ASCII/
          +-HG-Focus.CDF
      Mapping10K\_Xba131/
        1.XDA/
          +-Mapping10K\_Xba131.CDF
        3.ASCII/
          +-Mapping10K\_Xba131.CDF
      Test3/
        +-Test3.PSI
        1.XDA/
          +-Test3.CDF
        3.ASCII/
          +-Test3.CDF
  rawData/
    FusionSDK\_HG-Focus/
      HG-Focus/
        +-HG-Focus-1-121502.EXP
        +-HG-Focus-2-121502.EXP
        1.XDA/
          +-HG-Focus-1-121502.CHP
          +-HG-Focus-2-121502.CHP
        2.Calvin/
          +-HG-Focus-1-121502.CEL
          +-HG-Focus-1-121502.CHP
          +-HG-Focus-2-121502.CEL
          +-HG-Focus-2-121502.CHP
        3.ASCII/
          +-HG-Focus-1-121502.CEL
          +-HG-Focus-2-121502.CEL
    FusionSDK\_HG-U133A/
      HG-U133A/
        2.Calvin/
          +-ethan1-1.CEL
    FusionSDK\_Test3/
      Test3/
        +-Test3-1-121502.EXP
        +-Test3-2-121502.EXP
        1.XDA/
          +-Test3-1-121502.CHP
          +-Test3-2-121502.CHP
        2.Calvin/
          +-Test3-1-121502.CEL
          +-Test3-1-121502.CHP
          +-Test3-2-121502.CEL
          +-Test3-2-121502.CHP
        3.ASCII/
          +-Test3-1-121502.CEL
          +-Test3-2-121502.CEL
\end{alltt}
\end{Section}
\begin{Section}{License}
LGPL version 2.1 according to [1].
\end{Section}
\begin{Author}\relax
Adopted from [1] by
Henrik Bengtsson, \email{hb@stat.berkeley.edu},
James Bullard, \email{bullard@stat.berkeley.edu} and
Kasper Daniel Hansen, \email{khansen@stat.berkeley.edu}.
\end{Author}
\begin{References}\relax
[1] Affymetrix Inc, Fusion Software Developers Kit (SDK), 2007.
\url{http://www.affymetrix.com/support/developer/fusion/}\\
\end{References}

