\HeaderA{justMAS}{Generate Expression calls using a C implementation of the MAS 5.0 Algorithm}{justMAS}
\keyword{misc}{justMAS}
\begin{Description}\relax
Implements the MAS5.0 background correction, expression summary and scaling functions as described in Affy's
'Statistical Algorithms Description Document'
\end{Description}
\begin{Usage}
\begin{verbatim}
  justMAS(unnormalised,tgt=100,scale=TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{unnormalised}] An unnormalised AffyBatch object 
\item[\code{tgt}] The target intensity to scale array to, if scaling.
\item[\code{scale}] Scale the data to the specified target intensity.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Uses a C code implementation of the MAS5.0 algorithm (As described in Affymetrix's 'Statistical Algorithms Reference Guide' - see 
\url{http://www.affymetrix.com}, and in Hubbell et al. (2002) Robust Estimators for expression analysis. Bioinformatics 18(12) 1585-1592).
Note that this function returns log2 data.
\end{Details}
\begin{Value}
An AffyBatch object, with, in addition, scale-factors for each array stored in the object's \code{description@preprocessing@sfs} slot, and the target intensity the arrays were scaled to in  \code{description@preprocessing@tgt}
\end{Value}
\begin{Author}\relax
Crispin J Miller
\end{Author}
\begin{References}\relax
\url{ http://bioinformatics.picr.man.ac.uk/}
\end{References}
\begin{SeeAlso}\relax
\url{http://www.affymetrix.com/support/technical/technotes/statistical_reference_guide.pdf}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode} 
   ## Not run: 
     eset.mas <- justMAS(eset.mas);    
   
## End(Not run)
\end{ExampleCode}
\end{Examples}