\HeaderA{sam2excel}{CSV file of a SAM object}{sam2excel}
\keyword{IO}{sam2excel}
\keyword{file}{sam2excel}
\begin{Description}\relax
Generates a csv file for a SAM object for the use in Excel. This csv file can contain 
general information as the number of differentially expressed genes and the estimated FDR,
and gene-specific information on the differentially expressed genes.
\end{Description}
\begin{Usage}
\begin{verbatim}
 sam2excel(object, delta, file, excel.version=1, n.digits = 3, what = "both", ll = FALSE,
        chip = "", quote = FALSE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] a SAM object
\item[\code{delta}] a numerical value specifying the Delta value
\item[\code{file}] character string naming the file in which the output should be
stored. Must have the suffix ".csv"
\item[\code{excel.version}] either \code{1} or \code{2}. If \code{excel.version=1} (default) a csv file
for the use in an Excel version with American standard settings (\code{sep=","} and 
\code{dec="."}) will be generated. If \code{excel.version=2} a csv file for the European
standard setting (\code{sep=";"} and \code{dec=","}) will be generated
\item[\code{n.digits}] integer specifying the number of decimal places used in the output
\item[\code{what}] either \code{"both"}, \code{"stats"} or \code{"genes"}. If \code{"stats"} general 
information will be shown. If \code{"genes"} gene-specific information will be given. 
If \code{"both"} both general and gene-specific information will be shown
\item[\code{ll}] logical indicating if both the locus links and the symbols of the genes will be added
to the output
\item[\code{chip}] character string naming the chip type used in this analysis. Must
be specified as in the meta-data section of Bioconductor (e.g., \code{"hgu133a"}
for the Affymetrix HG-U133A chip). Only needed if \code{ll=TRUE}. 
If the argument \code{data} in \code{sam(data, cl, ...)} has been specified 
by an \code{exprSet} object \code{chip} need not to be specified
\item[\code{quote}] logical indicating if character strings and factors should be surrounded by 
double quotes. For details see \code{?write.table}
\end{ldescription}
\end{Arguments}
\begin{Author}\relax
Holger Schwender, \email{holger.schw@gmx.de}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{SAM-class}{SAM.Rdash.class}}, \code{\LinkA{sam}{sam}}, \code{\LinkA{sam2html}{sam2html}}
\end{SeeAlso}