\HeaderA{normScaleLimma}{Scale adjust a cDNA Microarray Object}{normScaleLimma}
\keyword{classes}{normScaleLimma}
\begin{Description}\relax
This function loads a \code{\LinkA{maigesRaw}{maigesRaw}} or \code{\LinkA{maiges}{maiges}}
object and scale adjust (normalise between arrays) the data using
functions from \emph{limma} package.
\end{Description}
\begin{Usage}
\begin{verbatim}
normScaleLimma(obj=NULL, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{obj}] object of type \code{\LinkA{maigesRaw}{maigesRaw}} or
\code{\LinkA{maiges}{maiges}} to be  normalised.
\item[\code{...}] additional parameters for function
\code{\LinkA{normalizeBetweenArrays}{normalizeBetweenArrays}}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function for scale adjustment is entirely based on function
\code{\LinkA{normalizeBetweenArrays}{normalizeBetweenArrays}} from
\emph{limma} package. See the help page for this function to see how
to set the parameters. Pay attention to the 'vsn' method of scale
adjustment, that must be used alone.
\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{normalizeBetweenArrays}{normalizeBetweenArrays}}
from \emph{limma} package.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Loading the dataset
data(gastro)

## Doing the scale adjustment from median-absolute-value method (from
## limma)
gastro.norm = normScaleLimma(gastro.norm, method="scale")
boxplot(gastro.norm) ## To see the efect of adjustment

## To do VSN scale adjustment (from vsn package) use the command. Be
## carefull that this method adjust the variance along A values and not
## between chips!!
gastro.norm = normScaleLimma(gastro.raw2, method="vsn")
boxplot(gastro.norm) ## See the effect
\end{ExampleCode}
\end{Examples}

