\HeaderA{calcA}{Method calcA to calculate A values}{calcA}
\methaliasA{calcA.default}{calcA}{calcA.default}
\methaliasA{calcA.maigesRaw}{calcA}{calcA.maigesRaw}
\keyword{array}{calcA}
\begin{Description}\relax
Generic function \code{\LinkA{calcA}{calcA}} to calculate A values from
classes of  microarray data objects defined in this package.
\end{Description}
\begin{Usage}
\begin{verbatim}
calcA(object, ...)

## Default S3 method:
calcA(object, ...)

## S3 method for class 'maigesRaw':
calcA(object, bkgSub="subtract", ...)

\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] object of any class. But only some methods are defined
in this moment.
\item[\code{bkgSub}] character string indicating the type of background
subtraction. May be 'none', 'subtract', 'half', 'minimum',
'movingmin', 'edwards', 'normexp' or 'rma'. Uses limma and defaults
to 'subtract'.
\item[\code{...}] additional parameters for \code{\LinkA{calcA}{calcA}} method.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This method receive an object (at moment of class
\code{\LinkA{maiges}{maiges}}, \code{\LinkA{maigesRaw}{maigesRaw}} or
\code{\LinkA{maigesANOVA}{maigesANOVA}}) and returns the matrix of A values. For
objects of class \code{\LinkA{maigesRaw}{maigesRaw}} it uses the function
\code{\LinkA{backgroundcorrect}{backgroundcorrect}} from \emph{limma} package to do
background correction before the calculation of A values.
\end{Details}
\begin{Author}\relax
Gustavo H. Esteves <gesteves@vision.ime.usp.br>
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{backgroundcorrect}{backgroundcorrect}} in the limma package and \code{\LinkA{calcW}{calcW}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Loading the dataset
data(gastro)

calcA(gastro.raw)
calcA(gastro.norm)
\end{ExampleCode}
\end{Examples}

