\HeaderA{normOLIN}{Normalise a cDNA Microarray Object}{normOLIN}
\keyword{classes}{normOLIN}
\begin{Description}\relax
This function loads a \code{\LinkA{maigesRaw}{maigesRaw}} object and normalise it
using methods OLIN or OSLIM.
\end{Description}
\begin{Usage}
\begin{verbatim}
normOLIN(obj=NULL, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{obj}] object of type \code{\LinkA{maigesRaw}{maigesRaw}} to be normalised.
\item[\code{...}] additional parameters for function \code{\LinkA{olin}{olin}}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function for normalisation is entirely based on function
\code{\LinkA{olin}{olin}} from \emph{OLIN} package. This function
implements the methods OLIN and OSLIM, proposed by Futschich and
Crompton (2004). See help page for this function to discover how to
set the parameters.
\end{Details}
\begin{Value}
This function returns a \code{\LinkA{maiges}{maiges}} object.
\end{Value}
\begin{Author}\relax
Gustavo H. Esteves <\email{gesteves@vision.ime.usp.br}>
\end{Author}
\begin{References}\relax
Futschik, M. and Crompton, T. Model selection and efficiency testing
for normalization of cDNA microarray data, \bold{Genome Biology}, 5,
R60, 2004 (\url{http://genomebiology.com/2004/5/8/R60}).
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{olin}{olin}} from \emph{OLIN} package.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Loading the dataset
data(gastro)

## Doing the OLIN normalization. Pay attention because, this methods are
## very time consuming!
## Not run: 
gastro.norm = normOLIN(gastro.raw2) ## Without scale adjustment

gastro.norm = normOLIN(gastro.raw2, OSLIN=TRUE) ## With scale adj
## End(Not run)

\end{ExampleCode}
\end{Examples}

