\HeaderA{summarize}{Probe Set Summarizing Functions}{summarize}
\methaliasA{summarize.mas4}{summarize}{summarize.mas4}
\methaliasA{summarize.mas5}{summarize}{summarize.mas5}
\methaliasA{summarize.rma}{summarize}{summarize.rma}
\aliasA{xpsSummarize}{summarize}{xpsSummarize}
\aliasA{xpsSummarize-methods}{summarize}{xpsSummarize.Rdash.methods}
\keyword{manip}{summarize}
\begin{Description}\relax
Converts Affymetrix probe level data to expression levels by summarizing the probe set
values into one expression measure and a standard error for this summary.
\end{Description}
\begin{Usage}
\begin{verbatim}
summarize(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, select = "none", method = character(), option = "transcript", logbase = "0", exonlevel = "", params = list(), xps.scheme = NULL, add.data = TRUE, verbose = TRUE)

summarize.mas4(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, option = "transcript", exonlevel = "", xps.scheme = NULL, add.data = TRUE, verbose = TRUE)

summarize.mas5(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, option = "transcript", exonlevel = "", xps.scheme = NULL, add.data = TRUE, verbose = TRUE)

summarize.rma(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, option = "transcript", exonlevel = "", xps.scheme = NULL, add.data = TRUE, verbose = TRUE)

xpsSummarize(object, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{xps.data}] object of class \code{DataTreeSet}.
\item[\code{filename}] file name of ROOT data file.
\item[\code{filedir}] system directory where ROOT data file should be stored.
\item[\code{tmpdir}] optional temporary directory where temporary ROOT files should be stored.
\item[\code{update}] logical. If \code{TRUE} the existing ROOT data file \code{filename} will be updated.
\item[\code{select}] type of probes to select for summarization.
\item[\code{method}] summarization method to use.
\item[\code{option}] option determining the grouping of probes for summarization, one of 
\sQuote{transcript}, \sQuote{exon}, \sQuote{probeset}; exon arrays only.
\item[\code{logbase}] logarithm base as character, one of \sQuote{0}, \sQuote{log},
\sQuote{log2}, \sQuote{log10}.
\item[\code{exonlevel}] exon annotation level determining which probes should be used
for summarization; exon/genome arrays only.
\item[\code{params}] vector of parameters for summarization method.
\item[\code{xps.scheme}] optional alternative \code{SchemeTreeSet}.
\item[\code{add.data}] logical. If \code{TRUE} expression data will be included as slot \code{data}.
\item[\code{verbose}] logical, if \code{TRUE} print status information.
\item[\code{object}] object of class \code{DataTreeSet}.
\item[\code{...}] the arguments described above.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Converts Affymetrix probe level data to expression levels by summarizing the probe set
values into one expression measure and a standard error for this summary.

\code{xpsSummarize} is the \code{DataTreeSet} method called by function \code{summarize},
containing the same parameters.
\end{Details}
\begin{Value}
An \code{\LinkA{ExprTreeSet}{ExprTreeSet}}.
\end{Value}
\begin{Author}\relax
Christian Stratowa
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{express}{express}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## first, load ROOT scheme file and ROOT data file
scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

## RMA background
data.bg.rma <- bgcorrect.rma(data.test3,"tmp_Test3RMA",filedir=getwd(),tmpdir="",verbose=FALSE)
## normalize quantiles
data.qu.rma <- normalize.quantiles(data.bg.rma,"tmp_Test3RMA",filedir=getwd(),tmpdir="",update=TRUE,verbose=FALSE)
## summarize medianpolish
data.mp.rma <- summarize.rma(data.qu.rma,"tmp_Test3RMA",filedir=getwd(),tmpdir="",update=TRUE,verbose=FALSE)

## get expression data.frame
expr.rma <- exprs(data.mp.rma)
head(expr.rma)

## plot expression levels
if (interactive()) {
boxplot(data.mp.rma)
boxplot(log2(expr.rma[,3:6]))
}
\end{ExampleCode}
\end{Examples}

