\HeaderA{normalize}{Normalization wrapper for Codelink objects.}{normalize}
\keyword{documentation}{normalize}
\keyword{utilities}{normalize}
\begin{Description}\relax
Takes a Codelink object and applies normalization to intensity values.
\end{Description}
\begin{Usage}
\begin{verbatim}
    normalize(object, method = "quantiles", log.it = TRUE, preserve = FALSE,
                weights = NULL, verbose = FALSE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] an object of class "Codelink".
\item[\code{method}] method to use in normalization.
\item[\code{log.it}] logical; if data should be log2.
\item[\code{preserve}] logical; if Ri slot should be preserved.
\item[\code{weights}] weights vector for method CyclicLoess.
\item[\code{verbose}] should informative output be printed.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Currently supported methods include "loess", "quantiles" and "median".  
Median normalization is analogous to the default method applied for the 
manufacturer in the Codelink software. Loess is a modified version of 
CyclicLoess implemented in the affy package, allowing missing values and 
weights. Quantile normalization uses the normalizeQuantiles() function in the 
limma package.
\end{Details}
\begin{Value}
A Codelink object with normalized intensity values.
\end{Value}
\begin{Author}\relax
Diego Diez
\end{Author}
\begin{Examples}
\begin{ExampleCode}
## Not run: 
        data(codelink.example)
        # Background correction.
        codelink.example <- bkgdCorrect(codelink.example,
        method = "half")
        # Normalization.
        codelink.example <- normalize(codelink.example,
        method = "quantile")
## End(Not run)
\end{ExampleCode}
\end{Examples}

