\HeaderA{colorectal}{Colorectal array CGH dataset}{colorectal}
\aliasA{clones.info.ex}{colorectal}{clones.info.ex}
\aliasA{log2.ratios.ex}{colorectal}{log2.ratios.ex}
\aliasA{pheno.type.ex}{colorectal}{pheno.type.ex}
\keyword{datasets}{colorectal}
\begin{Description}\relax
The colorectal dataset is an object of class \code{\LinkA{aCGH}{aCGH}}. It
represents a collection of 124 array CGH profiles of primary
colorectal tumors and their derived attributes. Each sample was
measured on the BAC clone DNA microarray with approximate resolution
of 1.4 Mb per clone. There were approximately 2400 clones spotted on
the array and each clone was printed in triplicates located
immediately next to each other. Each array consisted of the 16 (4 by
4) subarrays. The clones were mapped on the July 03 UCSC freeze. There
were a number of the discrete and continious phenotypes associated
with the samples such as age, mutation status for various markers,
stage, location and so on. All images were quantified and
normalized by Dr. Taku Tokuyasu using custom image software SPOT and
postprocessing custom software SPROC.
\end{Description}
\begin{Usage}
\begin{verbatim}data(colorectal)\end{verbatim}
\end{Usage}
\begin{Source}\relax
These data were generated at Dr. Fred Waldman's lab at UCSF Cancer
Center by K. Nakao and K. Mehta. The manuscript describing the data
and the analysis are described in
High-resolution analysis of DNA copy number alterations in colorectal
cancer by array-based comparative genomic hybridization,
\emph{Carcinogenesis}, 2004, Nakao et. al.
\end{Source}
\begin{References}\relax
Nakao et. al., High-resolution analysis of DNA copy number
alterations in colorectal cancer by array-based comparative genomic
hybridization, \emph{Carcinogenesis}, 2004
Jain et. al, Fully automatic quantification of microarray image data,
\emph{Genome Research}, 2003
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{aCGH}{aCGH}}
\code{\LinkA{plotGenome}{plotGenome}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

data(colorectal)
## WARNING: plotting the heatmap takes some time
plot(colorectal)
plotGenome(colorectal[,1:2])

\end{ExampleCode}
\end{Examples}

