\HeaderA{maNorm2D}{2D spatial location normalization function}{maNorm2D}
\keyword{smooth}{maNorm2D}
\begin{Description}\relax
This function is used for 2D spatial location normalization, using the robust local regression function \code{\LinkA{loess}{loess}}.  It should be used as an argument to the main normalization function \code{\LinkA{maNormMain}{maNormMain}}.
\end{Description}
\begin{Usage}
\begin{verbatim}
maNorm2D(x="maSpotRow", y="maSpotCol", z="maM", g="maPrintTip", w=NULL,
subset=TRUE, span=0.4, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] Name of accessor method for spot row coordinates, usually \code{maSpotRow}.
\item[\code{y}] Name of accessor method for spot column coordinates, usually \code{maSpotCol}.
\item[\code{z}] Name of accessor method for spot statistics, usually the log-ratio \code{maM}.
\item[\code{g}] Name of accessor method for print-tip-group indices, usually \code{maPrintTip}.
\item[\code{w}] An optional numeric vector of weights.
\item[\code{subset}] A "logical" or "numeric" vector indicating the subset of points used to
compute the fits. 
\item[\code{span}] The argument \code{span} which controls the degree of
smoothing in the  \code{\LinkA{loess}{loess}} function.
\item[\code{...}] Misc arguments
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The spot statistic named in \code{z} is regressed on spot row and column coordinates, separately within print-tip-group, using the \code{\LinkA{loess}{loess}} function.
\end{Details}
\begin{Value}
A function with bindings for the above arguments. This latter function takes as argument an object of class \code{"\LinkA{marrayRaw}{marrayRaw}"} (or possibly \code{"\LinkA{marrayNorm}{marrayNorm}"}), and returns a vector of fitted values to be substracted from the raw log-ratios. It calls the function \code{\LinkA{ma2D}{ma2D}}, which is not specific to microarray objects.
\end{Value}
\begin{Author}\relax
Sandrine Dudoit, \url{http://www.stat.berkeley.edu/~sandrine}.
\end{Author}
\begin{References}\relax
S. Dudoit and Y. H. Yang. (2002). Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In G. Parmigiani, E. S. Garrett, R. A. Irizarry and S. L. Zeger, editors, \emph{The Analysis of Gene Expression Data: Methods and Software}, Springer, New York.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{maNormMain}{maNormMain}}, \code{\LinkA{ma2D}{ma2D}}, \code{\LinkA{loess}{loess}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# See examples for maNormMain.

\end{ExampleCode}
\end{Examples}