\HeaderA{read.affy}{Read a Set of .CEL Files and Phenotypic Data}{read.affy}
\keyword{misc}{read.affy}
\begin{Description}\relax
Reads the specified file, which defines phenotypic data for a
set of .CEL files. Reads the specified files into an \code{\LinkA{AffyBatch}{AffyBatch}} object and
then creates a \code{\LinkA{phenoData}{phenoData}} object, defining the experimental factors 
for those chips.
\end{Description}
\begin{Usage}
\begin{verbatim}
read.affy(covdesc = "covdesc",path=".", ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{covdesc}] A white space delimited file suitable for reading as a \code{\LinkA{data.frame}{data.frame}}. The first column (with no column name)  
contains the names(or paths to) the .CEL files to read. Remaining columns (with names) represent experimental factors
for each chip. these become elements of the \code{\LinkA{phenoData}{phenoData}} object.

\item[\code{...}] extra functions to pass on to \code{ReadAffy} 
\item[\code{path}] The path to prefix the filenames with before calling \code{ReadAffy} 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\end{Details}
\begin{Value}
An AffyBatch object
\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{ReadAffy}{ReadAffy}}, \code{\LinkA{AffyBatch}{AffyBatch}} \code{\LinkA{data.frame}{data.frame}} \code{\LinkA{phenoData}{phenoData}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode} 
  ## Not run: 
    eset <- read.affy(); # read a set of CEL files
    eset.rma <- call.exprs(eset,"rma");   
  
## End(Not run)
\end{ExampleCode}
\end{Examples}