\HeaderA{lumiN}{Between chip normalization of a LumiBatch object}{lumiN}
\keyword{methods}{lumiN}
\begin{Description}\relax
A main function of between chip normalization of a LumiBatch object. Currently, four methods ("rsn", "ssn", "quantile", "loess", "vsn") are supported.
\end{Description}
\begin{Usage}
\begin{verbatim}
lumiN(x.lumi, method = c("quantile", "rsn", "ssn", "loess", "vsn"), verbose = TRUE, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x.lumi}] an ExpressionSet inherited object or a data matrix with columns as samples and rows as genes
\item[\code{method}] four different between chips normalization methods ("quantile", "rsn", "ssn", "loess", "vsn") are supported 
\item[\code{verbose}] a boolean to decide whether to print out some messages 
\item[\code{...}] other parameters used by corresponding method 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
lumiN is an interface for different normalization methods. Currently it supports "RSN" (See \code{\LinkA{rsn}{rsn}}), "SSN" (See \code{\LinkA{ssn}{ssn}}), "loess" (See \code{\LinkA{normalize.loess}{normalize.loess}}), "quantile" (See \code{\LinkA{normalize.quantiles}{normalize.quantiles}}) and "VSN" (See \code{\LinkA{vsn}{vsn}}). See details in individual functions. Note: the "VSN" normalization should be directly applied to the raw data instead of the lumiT processed data.
\end{Details}
\begin{Value}
Return an object with expression values normalized. The class of the return object is the same as the input object x.lumi.
If it is a LumiBatch object, it also includes the VST transform function and its parameters as attributes: "transformFun", "parameter". See \code{\LinkA{inverseVST}{inverseVST}} for details.
\end{Value}
\begin{Author}\relax
Pan Du, Simon Lin
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{rsn}{rsn}}, \code{\LinkA{ssn}{ssn}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## load example data
data(example.lumi)

## Do lumi transform
lumi.T <- lumiT(example.lumi)

## Do lumi between chip normaliazation
lumi.N <- lumiN(lumi.T, method='rsn', ifPlot=TRUE)

\end{ExampleCode}
\end{Examples}

