\HeaderA{find.params.pdnn}{A function to find the experiment specific PDNN parameters}{find.params.pdnn}
\keyword{manip}{find.params.pdnn}
\begin{Description}\relax
A function to find the paramaters specific to the chips in an
AffyBatch object.
\end{Description}
\begin{Usage}
\begin{verbatim}
find.params.pdnn(abatch, params.chiptype, optim.method = "BFGS", verbose = TRUE, give.warnings=TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{abatch}] an instance of \code{\LinkA{Affybatch-class}{Affybatch.Rdash.class}}. 
\item[\code{params.chiptype}] chip-type specific parameters (see details)
\item[\code{optim.method}] method for the optimization function
\code{\LinkA{optim}{optim}}. When \code{FALSE}, a steepest-descent method of our own
is used.
\item[\code{verbose}] verbosity (\code{TRUE} or \code{FALSE}) 
\item[\code{give.warnings}] report probeset IDs in the \code{abatch} that could not be found in
the \code{params.chiptype}
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function fits PDNN parameters that are specific to experimental
values. The parameters common to all the chips of a certain type
are returned by the function \code{\LinkA{pdnn.params.chiptype}{pdnn.params.chiptype}}.
If \code{NULL}, the parameter files included in the
package will be used whenever possible...
\end{Details}
\begin{Value}
A list of
\begin{ldescription}
\item[\code{lambda}] The lambda's
\item[\code{Bs}] The B's
\item[\code{Ns}] The N's
\item[\code{Fs}] The F's
\end{ldescription}
\end{Value}
\begin{References}\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{References}
\begin{SeeAlso}\relax
\code{\LinkA{pdnn.params.chiptype}{pdnn.params.chiptype}}, \code{\LinkA{generateExprVal.method.pdnn}{generateExprVal.method.pdnn}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## load a chip-specific parameter file
## (as returned by the function pdnn.params.chiptype)
data(hgu95av2.pdnn.params)

## load experimental data
library(affydata)
data(Dilution)

## one CEL to go faster
afbatch <- Dilution[, 1]
params <- find.params.pdnn(afbatch, hgu95av2.pdnn.params, optim.method =
FALSE, give.warnings=FALSE)

\end{ExampleCode}
\end{Examples}

