\HeaderA{hgu133a.pdnn.params}{Chip-type specific data}{hgu133a.pdnn.params}
\aliasA{chiptype.pdnn.params}{hgu133a.pdnn.params}{chiptype.pdnn.params}
\aliasA{hgu95av2.pdnn.params}{hgu133a.pdnn.params}{hgu95av2.pdnn.params}
\aliasA{pdnn-energy-parameter\_hg-u95av2}{hgu133a.pdnn.params}{pdnn.Rdash.energy.Rdash.parameter.Rul.hg.Rdash.u95av2}
\keyword{datasets}{hgu133a.pdnn.params}
\begin{Description}\relax
Chip-type specific data structure.
\end{Description}
\begin{Usage}
\begin{verbatim}
data(hgu95av2.pdnn.params)
\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format is a list:
\describe{
\item[Eg] environment (one entry per dinucleotide)
\item[Wg] numerical vector.
\item[En] environment (one entry per dinucleotide)
\item[Wn] numerical vector.
\item[gene.Sn] list (one entry per affyID)
\item[gene.Sg] list (one entry per affyID)
\item[gene.xy] list (one entry per affyID)
\item[params.gene] environment
}
\end{Format}
\begin{Details}\relax
These chip-specific data structures are generated from the data files
made available by the author of the PDNN paper (see the section source). They
are stored as \code{data} to save some computation time.
The data structures were made using the function
\code{\LinkA{pdnn.params.chiptype}{pdnn.params.chiptype}}. The data files are included in the
the directory `data' of the package.
\end{Details}
\begin{Note}\relax
To lower the size of the package, the only chip-specific data structures
included in the package is the one for HG-U95Av2.
\end{Note}
\begin{Source}\relax
Li Zhang, Michael F. Miles and Kenneth D. Aldape - A model of molecular interactions on short oligonucleotide
arrays, 2003, Nature Biotech., vol. 21, n.7
\end{Source}
\begin{Examples}
\begin{ExampleCode}
## give the path the original energy parameter files included in the package
list.files(system.file("exampleData", package="affypdnn"),
           "^pdnn-energy-parameter_", full.names=TRUE)
\end{ExampleCode}
\end{Examples}

