\HeaderA{normLoc}{Normalise a cDNA Microarray Object}{normLoc}
\keyword{classes}{normLoc}
\begin{Description}\relax
This function loads a \code{\LinkA{maigesRaw}{maigesRaw}} object and corrects for
location bias.
\end{Description}
\begin{Usage}
\begin{verbatim}
normLoc(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{normalizeWithinArrays}{normalizeWithinArrays}} from \emph{limma} package.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function for normalisation is entirely based on the function
\code{\LinkA{normalizeWithinArrays}{normalizeWithinArrays}} from \emph{limma}
package. See their help page to known how to setup the parameters
correctly. The parameters \code{layout} and \code{weights}, are
automatically specified by the object \code{obj} and must not be specified.
\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{SeeAlso}\relax
\code{\LinkA{normalizeWithinArrays}{normalizeWithinArrays}} from \emph{limma} package.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Loading the dataset
data(gastro)

## Do the normalization by loess method and span 0.4
gastro.norm = normLoc(gastro.raw2, span=0.4, method="loess")

## Do the same normalization without background subtraction
gastro.norm = normLoc(gastro.raw2, span=0.4, method="loess", bc.method="none")
\end{ExampleCode}
\end{Examples}

