\HeaderA{readCel2eSet}{Read celfiles into an ExpressionSet object.}{readCel2eSet}
\keyword{manip}{readCel2eSet}
\begin{Description}\relax
This is a wrapper for \code{\LinkA{ReadAffy}{ReadAffy}} that
returns an \code{\LinkA{ExpressionSet}{ExpressionSet}} object rather than an
AffyBatch. This is particularly usefiles for arrays for which we have
or need no CDF environment.
\end{Description}
\begin{Usage}
\begin{verbatim}
readCel2eSet(filename, adf, path=".", rotated=FALSE, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{filename}] Character vector with CEL file names. Either
\code{filename} or \code{adf} need to be specified, but not both.
\item[\code{adf}] Object of class
\code{\LinkA{AnnotatedDataFrame}{AnnotatedDataFrame}}.
\item[\code{path}] Character scalar with path to CEL files.
\item[\code{rotated}] Logical scalar, see details.
\item[\code{...}] Further arguments that are passed on to
\code{new("ExpressionSet")}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The \code{rotate} options allows to deal with different versions of
the scanner software. Older versions rotated the image by 90 degrees,
newer ones do not. Use the default \code{rotated=FALSE} for CEL files
produced by the newer version.
\end{Details}
\begin{Value}
\code{\LinkA{ExpressionSet}{ExpressionSet}} object.
\end{Value}
\begin{Author}\relax
W. Huber
\end{Author}
\begin{Examples}
\begin{ExampleCode}
## To test the rotation, look at the scatterplot between two DNA hybes
## that were measured with scanner software that rotated (041120) and did
## not rotate (060125)
##
## cp /ebi/research/huber/Projects/tilingArray/Celfiles/041120_S96genDNA_re-hybe.cel.gz ~/p/tmp
## cp /ebi/research/huber/Projects/allelicTranscription/celfiles_allelictrans/060125_S96_genomicDNA.zip ~/p/tmp
## cd ~/p/tmp
## gunzip 041120_S96genDNA_re-hybe.cel.gz
## unzip 060125_S96_genomicDNA.zip
##
## Not run: 
library("affy")
library("geneplotter")
options(error=recover)

e1 = readCel2eSet("041120_S96genDNA_re-hybe.cel", rotated=TRUE)
e2 = readCel2eSet("060125_S96_genomicDNA.CEL")

smoothScatter(log(exprs(e1)), log(exprs(e2)), nrpoints=0)
## End(Not run)
\end{ExampleCode}
\end{Examples}

