\HeaderA{read.cel.intensities}{Reads the intensities contained in several Affymetrix CEL files}{read.cel.intensities}
\keyword{file}{read.cel.intensities}
\begin{Description}\relax
Reads the intensities of several Affymetrix CEL files (as opposed to
\code{read.cel.complete} which only reads a single file).
\end{Description}
\begin{Usage}
\begin{verbatim}
read.cel.intensities(fnames, indices = NULL, verbose = 0)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{fnames}] 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{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{fnames} argument.
\end{Value}
\begin{Note}\relax
Currently this function builds on \code{read.cel.complete}, 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{read.cel.complete}{read.cel.complete}} for the a discussion of a more
versatile function, particular with details of the \code{indices}
argument.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Not run: 
read.cel.intensities(fnames = c("~/testFile1.CEL", "~/testFile2.CEL"))
## End(Not run)
\end{ExampleCode}
\end{Examples}

