\HeaderA{read.affybatch2}{Read CEL files into an Affybatch}{read.affybatch2}
\keyword{file}{read.affybatch2}
\begin{Description}\relax
Read CEL files into an Affybatch. An implemetation build on the
\pkg{affxparser} package.
\end{Description}
\begin{Usage}
\begin{verbatim}
read.affybatch2(..., filenames = character(0),
                phenoData = new("phenoData"),
                description = NULL, notes = "",
                compress = getOption("BioC")$affy$compress.cel,
                rm.mask = FALSE, rm.outliers = FALSE,
                rm.extra = FALSE, verbose = FALSE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{...}] file names separated by comma.
\item[\code{filenames}] file names in a character vector.
\item[\code{phenoData}] a \code{phenoData} object
\item[\code{description}] a \code{MIAME} object
\item[\code{notes}] notes.
\item[\code{compress}] Not currently supported.
\item[\code{rm.mask}] Not currently supported.
\item[\code{rm.outliers}] Not currently supported.
\item[\code{rm.extra}] Not currently supported.
\item[\code{verbose}] verbosity flag.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\end{Details}
\begin{Value}
An \code{AffyBatch} object.
\end{Value}
\begin{Author}\relax
The author of the original \code{read.affybatch} function:
Ben Bolstad, \email{bolstad@stat.berkeley.edu} as well as 
James Bullard, \email{bullard@stat.berkeley.edu} and Kasper Daniel Hansen
\email{khansen@stat.berkeley.edu}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{read.affybatch}{read.affybatch}} in \pkg{affy} as well as
\code{\LinkA{read.cel.intensities}{read.cel.intensities}} and \code{\LinkA{read.cel.complete}{read.cel.complete}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
\end{ExampleCode}
\end{Examples}

