\HeaderA{readCelIntensities}{Reads the intensities contained in several Affymetrix CEL files}{readCelIntensities}
\keyword{file}{readCelIntensities}
\keyword{IO}{readCelIntensities}
\begin{Description}\relax
Reads the intensities of several Affymetrix CEL files (as opposed to
\code{readCel}() which only reads a single file).
\end{Description}
\begin{Usage}
\begin{verbatim}
 readCelIntensities(filenames, indices = NULL, ..., verbose = 0)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{filenames}] the names of the CEL files as a character vector.
\item[\code{indices}] a vector of which indices should be read. If the argument
is \code{NULL} all features will be returned.
\item[\code{...}] Additional arguments passed to \code{readCel}().
\item[\code{verbose}] an integer: how verbose do we want to be, higher means
more verbose.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The function will initially allocate a matrix with the same
memory footprint as the final object.
\end{Details}
\begin{Value}
A matrix with a number of rows equal to the length of the
\code{indices} argument (or the number of features on the entire
chip), and a number of columns equal to the number of files. The
columns are ordered according to the \code{filenames} argument.
\end{Value}
\begin{Note}\relax
Currently this function builds on \code{readCel}(), and simply
calls this function multiple times. If testing yields sufficient
reasons for doing so, it may be re-implemented in C++.
\end{Note}
\begin{Author}\relax
James Bullard, \email{bullard@stat.berkeley.edu} and
Kasper Daniel Hansen, \email{khansen@stat.berkeley.edu}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{readCel}{readCel}}() for a discussion of a more versatile function,
particular with details of the \code{indices} argument.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  # Scan current directory for CEL files
  files <- list.files(pattern="[.](c|C)(e|E)(l|L)$")
  if (length(files) >= 2) {
    cel <- readCelIntensities(files[1:2])
    str(cel)
    rm(cel)
  }

  # Clean up
  rm(files)
\end{ExampleCode}
\end{Examples}

