\HeaderA{data.raw}{Example data for the dyebias package}{data.raw}
\aliasA{data.norm}{data.raw}{data.norm}
\keyword{datasets}{data.raw}
\begin{Description}\relax
The \code{dyebias}-package, described in Margaritis et al. (2009) can
be used to get rid of dye bias in two-colour microarrays. The
\code{data.raw} and \code{data.norm} objects are used in its examples.

The objects represent four hybridizations of identical mRNA, with
increasing Cy3 and Cy5 labeling percentages (identical per slide) and
differently spiked-in external controls to judge the process of
dyebias correction.
\end{Description}
\begin{Usage}
\begin{verbatim}
       data(data.raw)
       data(data.norm)
\end{verbatim}
\end{Usage}
\begin{Format}\relax
The data uses the \code{marray}-package by Dudoit and Yang (2002).
\code{data.raw} is a \code{marrayRaw} object, \code{data.norm} is a
\code{marrayNorm} object derived from it by print-tip LOESS
normalization. Neither is dyebias-corrected yet.
\end{Format}
\begin{Details}\relax
The column \code{R.group} of \code{maInfo(maTargets(data.norm))}
shows the details. Eg.,  \code{4\%\_2EC} indicates that the labeling
(of both channels) was at 4\%, and the external controls were spiked
in at a concentration twice that of the green channel. See Margaritis
et\textasciitilde{}al. (2009) for details.
\end{Details}
\begin{Note}\relax
The Tuteja data is also included in this package under the
(inst)/doc directory, as this data is not proper rda, tab or csv
data. For details, refer to the original publication and/or the
\code{dyebias} vignette.
\end{Note}
\begin{Author}\relax
Philip Lijnzaad
\end{Author}
\begin{Source}\relax
All accession numbers below refer to ArrayExpress (http://www.ebi.ac.uk/microarray).

This two-colour microarrray data was obtained from identical mRNA
extracts (protocol P-UMCU-37), spiked with external controls,
dUTP-labeled with Cy3 and Cy5 (protocol P-UMCU-38). This was
hybridized (protocol P-UMCU-39) onto self-spotted slides containing
70-mer oligonucleotides (2 replicates per oligo, Operon "Array-Ready",
and including 2838 control features; protocol P-UMCU-34).  Scanning
was done with an Agilent G2565AA scanner (protocol P-UMCU-40) and
images were quantified with BioDiscovery's ImaGene 7.x (protocol
P-UMCU-42)
\end{Source}
\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}

Dudoit, S. and Yang, Y.H. (2002)  Bioconductor R packages for
exploratory analysis and normalization of cDNA microarray data. In:
Parmigiani, G., Garrett, E.S. , Irizarry, R.A., and Zeger, S.L. (eds.)
\emph{The Analysis of Gene Expression Data: Methods and Software},
New\textasciitilde{}York: Springer
\end{References}
\begin{Examples}
\begin{ExampleCode}
  data(data.raw)
  data(data.norm)
\end{ExampleCode}
\end{Examples}

