\HeaderA{normScaleMarray}{Scale adjust a cDNA Microarray Object}{normScaleMarray}
\keyword{classes}{normScaleMarray}
\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{marray} package.
\end{Description}
\begin{Usage}
\begin{verbatim}
normScaleMarray(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{maNormScale}{maNormScale}}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function for scale adjustment is entirely based on function
\code{\LinkA{maNormScale}{maNormScale}} from \emph{marray} package. See the
help page for this function to see how to set the parameter. Pay
attention to the \code{subset} argument that is fixed directly from
the \code{UseSpots} and \code{BadSpots} from \code{obj} object, and
must not be specified in the additional arguments.

The functionality of the scale adjustment function from \emph{marray}
package was added because it uses an estimator of MAD different from
that one used in \emph{limma} package. Also, using 
\code{\LinkA{maNormScale}{maNormScale}} function it is possible to do print
tip scale adjustment.
\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{maNormScale}{maNormScale}} from \emph{marray} package.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Loading the dataset
data(gastro)

## Doing global MAD scale adjustment
gastro.norm = normScaleMarray(gastro.norm, norm="globalMAD")
boxplot(gastro.norm) ## To see the effect of MAD adjustment

## For print tip MAD use the following command
## Not run: 
gastro.norm = normScaleMarray(gastro.norm, norm="printTipMAD")
## End(Not run)
\end{ExampleCode}
\end{Examples}

