\HeaderA{dyebias.umcu.proper.estimators}{Determine which spots should not be ruled out as slide bias estimators}{dyebias.umcu.proper.estimators}
\keyword{misc}{dyebias.umcu.proper.estimators}
\begin{Description}\relax
Some spots (reporters/probes) should not be used when estimating the slide
bias. Typical examples are mitochondrial genes and spots known to
cross-hybridize. This function finds the ones that are OK to use.
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{reporter.info}] A data.frame, one row per spot, with (at least) columns \code{reporterId}
(e.g. gene id or oligo id) and any of the following
characteristics: \code{reporterGroup, chromosomeName, bioSeqType,
    crosshybRank and reporterSequence}.  They are used to get
rid of reporters that are not suitable when estimating the slide
bias.

\item[\code{verbose}] Logical speficying whether to be verbose or not 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function is particular to the slides and database set-up at the
Holstege lab, but might serve as inspiration.
\end{Details}
\begin{Value}
Returns and index vector that can be
used as the \code{estimator.subset}-argument to
\code{dyebias.application.subset}.
\end{Value}
\begin{Author}\relax
Philip Lijnzaad \email{p.lijnzaad@umcutrecht.nl}
\end{Author}
\begin{References}\relax
Margaritis, T., Lijnzaad, P., van\textasciitilde{}Leenen, D., Bouwmeester, D.,
Kemmeren, P., van\textasciitilde{}Hooff, S.R and Holstege, F.C.P. (2009)
Adaptable gene-specific dye bias correction for two-channel DNA microarrays.
\emph{Molecular Systems Biology, submitted}
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{dyebias.apply.correction}{dyebias.apply.correction}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

  

  ### choose the estimators and which spots to correct:
  estimator.subset <- dyebias.umcu.proper.estimators(maInfo(maGnames(data.norm)))

  summary(estimator.subset)

  ### do the correction
  ## Not run: 
     correction <- dyebias.apply.correction(data.norm=data.norm,
                                         iGSDBs = iGSDBs.estimated,
                                         estimator.subset=estimator.subset,
                                         application.subset = TRUE,
                                         verbose=TRUE)
   
## End(Not run)
\end{ExampleCode}
\end{Examples}

