\HeaderA{call.exprs}{Generate Expression Summaries for Affymetrix Data}{call.exprs}
\keyword{misc}{call.exprs}
\begin{Description}\relax
Generates expression summaries and normalizes Affymetrix data using either MAS5.0, GCRMA or RMA algorithms.
\end{Description}
\begin{Usage}
\begin{verbatim}
call.exprs(x, algorithm = "rma", do.log = TRUE, sc = 100, method = NA)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] an \code{AffyBatch} object 
\item[\code{algorithm}] one of '"rma","rma-R","gcrma", "mas5", "mas5-R". "rma" and "mas5" make use of a native C-library and are faster than "rma-R" and "mas5-R". 
\item[\code{do.log}] return logged data if true 
\item[\code{sc}] if the mas5 algorithm is being used, sets the target intensity to which the chips should be scaled. 
\item[\code{method}] The algorithm used to normalise the data. Has no effect for "rma", 
defaults to quantile normalisation for "rma" and no normalisation for "mas5" 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\end{Details}
\begin{Value}
An AffyBatch object containing expression summaries.
\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
\code{\LinkA{read.affy}{read.affy}}, \code{\LinkA{expresso}{expresso}}, \code{\LinkA{justRMA}{justRMA}}, \code{\LinkA{justMAS}{justMAS}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode} 
  ## Not run: 
    eset.rma  <- call.exprs(eset,"rma"); 
    eset.mas5 <- call.exprs(eset,"mas5"); 
  
## End(Not run)
\end{ExampleCode}
\end{Examples}