\HeaderA{lumiExpresso}{From raw Illumina probe intensities to expression values}{lumiExpresso}
\keyword{methods}{lumiExpresso}
\begin{Description}\relax
Goes from raw Illumina probe intensities to expression values
\end{Description}
\begin{Usage}
\begin{verbatim}
lumiExpresso(lumiBatch, bg.correct = TRUE, bgcorrect.param = list(method='bgAdjust'), variance.stabilize = TRUE, 
        varianceStabilize.param = list(), normalize = TRUE, normalize.param = list(), QC.evaluation = TRUE, 
        QC.param = list(), verbose = TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{lumiBatch}] a LumiBatch object, which can be the return of \code{\LinkA{lumiR}{lumiR}} 
\item[\code{bg.correct}] a boolean to decide whether to do background correction or not 
\item[\code{bgcorrect.param}] a list of parameters of \code{\LinkA{lumiB}{lumiB}} 
\item[\code{variance.stabilize}] a boolean to decide whether to do variance stabilization or not 
\item[\code{varianceStabilize.param}] a list of parameters of \code{\LinkA{lumiT}{lumiT}} 
\item[\code{normalize}] a boolean to decide whether to do normalization or not 
\item[\code{normalize.param}] a list of parameters of \code{\LinkA{lumiN}{lumiN}} 
\item[\code{QC.evaluation}] a boolean to decide whether to do quality control estimation before and after preprocessing 
\item[\code{QC.param}] a list of parameters of \code{\LinkA{lumiQ}{lumiQ}} 
\item[\code{verbose}] a boolean to decide whether to print out some messages 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The function is to encapsulate the major functions of Illumina preprocessing. It is organized in a similar way as the \code{\LinkA{expresso}{expresso}} function in affy package.
\end{Details}
\begin{Value}
return a processed LumiBatch object. The operation history can be track in the history slot of the object.
\end{Value}
\begin{Author}\relax
Pan Du
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{lumiB}{lumiB}}, \code{\LinkA{lumiT}{lumiT}}, \code{\LinkA{lumiN}{lumiN}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## load example data
data(example.lumi)

## Do all the default preprocessing in one step
lumi.N <- lumiExpresso(example.lumi)

## Do customized preprocessing. No variance stabilizing or log transform, use Quantile normalization.
lumi.N <- lumiExpresso(example.lumi, variance.stabilize=FALSE, normalize.param = list(method='quantile'))

\end{ExampleCode}
\end{Examples}

