\HeaderA{spatial}{Examples of  array-CGH data with spatial artifacts}{spatial}
\aliasA{edge}{spatial}{edge}
\methaliasA{edge.norm}{spatial}{edge.norm}
\methaliasA{edge.txt}{spatial}{edge.txt}
\aliasA{gradient}{spatial}{gradient}
\methaliasA{gradient.gpr}{spatial}{gradient.gpr}
\methaliasA{gradient.norm}{spatial}{gradient.norm}
\keyword{datasets}{spatial}
\begin{Description}\relax
This data set provides an example of array-CGH data with spatial
artifacts, consisting of including \code{\LinkA{arrayCGH}{arrayCGH}}
objects before and after normalization
\end{Description}
\begin{Usage}
\begin{verbatim}data(spatial)\end{verbatim}
\end{Usage}
\begin{Format}\relax
\item[edge, gradient] \code{\LinkA{arrayCGH}{arrayCGH}}
objects before normalization:
\Tabular{lll}{
& \code{arrayValues} & spot-level information \\
& \code{arrayDesign} & block design of the array \\
& \code{cloneValues} & additionnal clone-level data (chromosome,
position) \\
}

\item[edge.norm, gradient.norm] \code{\LinkA{arrayCGH}{arrayCGH}}
objects after normalization
\end{Format}
\begin{Details}\relax
'edge' presents local spatial bias in the top-right edge corner, and
'gradient' presents global spatial trend. 'edge' and 'gradient' are
\code{\LinkA{arrayCGH}{arrayCGH}} objects before normalization. They have
been created respectively from spot and gpr files using
\code{\LinkA{import}{import}}. 'edge.norm' and 'gradient.norm' are the
corresponding \code{\LinkA{arrayCGH}{arrayCGH}} objects after normalization
using \code{\LinkA{norm.arrayCGH}{norm.arrayCGH}}.

\code{\LinkA{flag}{flag}} objects used for data normalization come from
\code{\LinkA{flags}{flags}} dataset.
\end{Details}
\begin{Note}\relax
People interested in tools for array-CGH analysis can
visit our web-page: \url{http://bioinfo.curie.fr}.
\end{Note}
\begin{Author}\relax
Pierre Neuvial, \email{manor@curie.fr}.
\end{Author}
\begin{Source}\relax
Institut Curie, \email{manor@curie.fr}.
\end{Source}
\begin{SeeAlso}\relax
\code{\LinkA{flags}{flags}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(spatial)

## edge: example of array with local spatial effects

layout(matrix(1:4, 2, 2), height=c(9,1))
arrayPlot(edge, "LogRatio", main="Log-ratios before normalization",
zlim=c(-1,1), bar="h", layout=FALSE, mediancenter=TRUE)
arrayPlot(edge.norm, "LogRatioNorm", main="Log-ratios after spatial
normalization", zlim=c(-1,1), bar="h", layout=FALSE, mediancenter=TRUE) 

## gradient: example of array with spatial gradient

layout(matrix(1:4, 2, 2), height=c(9,1))
arrayPlot(gradient, "LogRatio", main="Log-ratios before normalization",
zlim=c(-2,2), bar="h", layout=FALSE)
arrayPlot(gradient.norm, "LogRatioNorm", main="Log-ratios after spatial
normalization", zlim=c(-2,2), bar="h", layout=FALSE)   
\end{ExampleCode}
\end{Examples}

