\HeaderA{PMindex}{Find the index of the exact match (PM) or background probes from a probeAnno environment}{PMindex}
\aliasA{BGindex}{PMindex}{BGindex}
\keyword{manip}{PMindex}
\begin{Description}\relax
Find the index of the exact match (PM) or background probes from a probeAnno environment
\end{Description}
\begin{Usage}
\begin{verbatim}
PMindex(probeAnno)
BGindex(probeAnno)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{probeAnno}] environment with probe annotations. See
package \code{davidTiling} for an example (?probeAnno).
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
These functions extract the exact match probes (PM) or background
probes (from intergenic regions outside of known annotations) indices from \code{probeAnno}.  
These indices can be used to select the relevant rows of intensity
data from the \code{ExpressionSet} object for plotting and normalization.
\end{Details}
\begin{Value}
Numeric vector of indices.
\end{Value}
\begin{Author}\relax
Matt Ritchie <ritchie@ebi.ac.uk>
\end{Author}
\begin{Examples}
\begin{ExampleCode}
## library(davidTiling)
## data(davidTiling)
## data(probeAnno)
## pmind <- PMindex(probeAnno)
## mmind <- MMindex(probeAnno)
## bgind <- BGindex(probeAnno)
## boxplot(as.data.frame(log2(exprs(davidTiling))[pmind,]), outline=FALSE)           
\end{ExampleCode}
\end{Examples}

