\HeaderA{bg.parameters.ns}{Estimation of non-specific Binding Background Parameters}{bg.parameters.ns}
\aliasA{average.for.PAV}{bg.parameters.ns}{average.for.PAV}
\aliasA{left.sigma}{bg.parameters.ns}{left.sigma}
\aliasA{PAV}{bg.parameters.ns}{PAV}
\keyword{manip}{bg.parameters.ns}
\begin{Description}\relax
An internal function to be used by \code{\LinkA{gcrma}{gcrma}}
\end{Description}
\begin{Usage}
\begin{verbatim}
bg.parameters.ns(x,affinities,affinities2,affinities3)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] PM or MM intensities after optical background correction, before non-specific-binding correction.
\item[\code{affinities}] Probe affinities for probes with known
sequences.Used to estimate the function between non-specific binding
and affinities.
\item[\code{affinities2}] Probe affinities for the probes whoes expected non-specific binding
intensity is to be predicted.

\item[\code{affinities3}] Probe affinities for another extra group of probes whoes expected non-specific binding
intensity is to be predicted.

\end{ldescription}
\end{Arguments}
\begin{Value}
a vector of same length as x.
\end{Value}
\begin{Author}\relax
Rafeal Irizarry, Zhijin (Jean) Wu
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{gcrma}{gcrma}}
\end{SeeAlso}