\HeaderA{normalizeByReference}{Probe-specific normalization of hybridization intensities from a short-oligo microarray}{normalizeByReference}
\keyword{manip}{normalizeByReference}
\begin{Description}\relax
Adjust the hybridization intensities from a short oligo microarray
for probe-specific response effect by using one or several reference hybridizations.
\end{Description}
\begin{Usage}
\begin{verbatim}
normalizeByReference(x, reference, pm, background, nrStrata=10,
  cutoffQuantile=0.05, plotFileNames, verbose=FALSE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] eSet containing the data to be normalized.
\item[\code{reference}] eSet with the same number of features as \code{x},
containing the reference signal.
\item[\code{pm}] indices specifying the perfect match features in
\code{reference}.
This can be either an integer vector with values between 1 and
\code{nrow(exprs(reference))} or a logical vector.
\item[\code{background}] indices specifying a set of background features in
\code{x}.
This can be either an integer vector with values between 1 and
\code{nrow(exprs(x))} or a logical vector.
\item[\code{nrStrata}] Integer (length 1), number of strata for the estimation of
the background function.
\item[\code{cutoffQuantile}] Numeric (length 1), the probes whose reference
signal is below this quantile are thrown out.
\item[\code{plotFileNames}] Character vector whose length is the same as the
number of arrays in \code{x}. Optional, if missing, no plots are
produced.
\item[\code{verbose}] Logical of length 1, if \code{TRUE}, some messages about
progress are printed.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The intensities in \code{x} are adjusted according to the
reference values. For example, the reference values could be obtained
by hybridizing a DNA sample to the array. The abundance of target is
thus the same for all PM probes, and the intensities that are actually
observed can be used for estimating the adjustment parameters. Since
this only makes sense for the PM probes, NA values be returned for all
other probes. The set of indices for background probes,
\code{background}, is used for the
estimation of the background correction.
\end{Details}
\begin{Value}
A copy of \code{x} with the normalized intensities.
\end{Value}
\begin{Author}\relax
W. Huber \email{huber@ebi.ac.uk}
\end{Author}
\begin{References}\relax
Transcript mapping with 
oligonucleotide high-density tiling arrays,
W. Huber, J. Toedling, L. Steinmetz, preprint (2006).
\end{References}
\begin{Examples}
\begin{ExampleCode}
  ## see vignette assessNorm.Rnw in inst/scripts directory
\end{ExampleCode}
\end{Examples}

