%\VignetteIndexEntry{kidpack - overview over the DKFZ kidney data package}
%\VignetteDepends{kidpack}
%\VignetteKeywords{Expression Analysis}
%\VignettePackage{kidpack}

\documentclass[11pt]{article}
\usepackage{geometry}

\newcommand{\Rfunction}[1]{\texttt{#1}}
\newcommand{\Robject}[1]{\texttt{#1}}
\newcommand{\Rpackage}[1]{\textit{#1}}
\newcommand{\Rclass}[1]{\textit{#1}}

\usepackage{/home/hpages/R-2.4.0/share/texmf/Sweave}
\begin{document}
\title{Overview over the DKFZ kidney data package}
\author{Wolfgang Huber}
\maketitle

\begin{Schunk}
\begin{Sinput}
> library(kidpack)
\end{Sinput}
\end{Schunk}
 
The package contains five data objects: two for the processed data, including
sample information (phenoData) and probe (genes) information, and three for
the raw data, including spotting information and array processing information.

The data was measured at the German Cancer Research Centre in 2002 by Holger
S\"ultmann~\cite{kidney3}. He hybridized labeled cDNA from around 85 renal
cell cancer biopsies that had been obtained at the University of G\"ottingen
to cDNA arrays that he had produced himself. The cDNA arrays use the two-color
Stanford-type spotted cDNA technology, with 4224 different clones spotted in
duplicate. About half of the clones were selected for being expressed in
kidney according to a previous study on whole genome arrays, and the other
half are from Bernd Korn's (RZPD) 'onco collection'. Each sample was
hybridized twice. 175 chips were scanned and digitized. After quality control,
we selected one representative (good) chip for each sample, resulting in a set
of 74. These are presented in the \Rclass{exprSet} named \Robject{eset}.

\section{What is it good for?}  

There were three different subtypes of renal cell cancer (RCC): clear cell
(cc), papillary (p), and chromophobe (ch). These pheno-variables may be used
for classification or differential expression. The gene expression is quite 
strongly associated with the subtype.

Other interesting phenovariables are the survival variables \Robject{(progress,
rf.survival)} and \Robject{(died, survival.time)}. Obviously, the two are highly
correlated. The binary variable \Robject{m} indicates whether metastases were
present (and known) at the time of surgery.  The association of the gene
expression data with these variables is more subtle. Perhaps only wishful
thinking.

The manuscript has been submitted. As soon as it is accepted, final, and
public, the preprint will be made availabe in the doc directory of the
package. Until then, please contact me (WH) directly and I can send you the most
current version by email.

\section{Processed data}
\begin{Schunk}
\begin{Sinput}
> data(eset)
> data(cloneanno)
\end{Sinput}
\end{Schunk}

For later use, we define some plot colors for the \Robject{type} variable:

\begin{Schunk}
\begin{Sinput}
> unique(pData(eset)$type)
\end{Sinput}
\begin{Soutput}
[1] "ccRCC" "pRCC"  "chRCC"
\end{Soutput}
\begin{Sinput}
> cols <- c("red", "blue", "darkgreen")
> names(cols) <- c("ccRCC", "pRCC", "chRCC")
\end{Sinput}
\end{Schunk}

The chips contained three different clones that all probed for 
Fibronection 1:
\begin{Schunk}
\begin{Sinput}
> sel <- grep("fibronectin 1", cloneanno$description)
> cloneanno[sel, ]
\end{Sinput}
\begin{Soutput}
     plate SrcRow SrcCol imageid       AccNumber spot1 spot2
2119     6     11      3  136798 r36450,"r36451"  1612  5964
2626     7     14     15  324061 w46461,"w46530"  1730  6082
2627     7     14     19  324997 w48576,"w48721"  1731  6083
                                                                description
2119  human mrna for fibronectin (fn precursor),"fibronectin 1 : fn1","fn1"
2626  human mrna for fibronectin (fn precursor),"fibronectin 1 : fn1","fn1"
2627  human mrna for fibronectin (fn precursor),"fibronectin 1 : fn1","fn1"
       vendor
2119 IMAGp950
2626 IMAGp950
2627 IMAGp950
\end{Soutput}
\end{Schunk}

Let's plot the expression values:

\begin{Schunk}
\begin{Sinput}
> eo <- eset[sel, order(pData(eset)$type)]
> x <- exprs(eo)
> plot(c(1, ncol(x)), range(x), type = "n")
> for (i in 1:nrow(x)) points(x[i, ], col = cols[pData(eo)$type], 
+     pch = 16)
\end{Sinput}
\end{Schunk}
\includegraphics{kidpack-fn2}

\section{Raw data}
Let's have a look at the raw data
\begin{Schunk}
\begin{Sinput}
> data(qua)
> data(hybanno)
> data(spotanno)
> s1 <- cloneanno$spot1[sel]
> s2 <- cloneanno$spot2[sel]
> s1
\end{Sinput}
\begin{Soutput}
[1] 1612 1730 1731
\end{Soutput}
\begin{Sinput}
> qua[s1, "fg.green", 1:3]
\end{Sinput}
\begin{Soutput}
           1       2       3
1612 23.2745  7.4989 12.4166
1730 18.4937 10.3098 16.4911
1731 17.2570  8.1597 12.4474
\end{Soutput}
\begin{Sinput}
> hybanno[1:3, ]
\end{Sinput}
\begin{Soutput}
             filename patientid slideid
1 00-P09206_E44-1.txt        87   E44-1
2 00-P09206_E63-3.txt        87   E63-3
3 00-U00363_E34-1.txt        86   E34-1
\end{Soutput}
\end{Schunk}

The columns \Robject{cloneanno\$spot1}, \Robject{cloneanno\$spot2} are of class
\Robject{numeric}, with values from 1 to 8704. They refer to the rows of
\Robject{spotannoanno}.

The column \Robject{spotanno\$probe} is of class \Robject{numeric}, with values
from 1 to 4224, referring to the rows of \Robject{cloneanno}.

\begin{thebibliography}{10}

\bibitem{kidney3}
Gene expression in kidney cancer is associated with novel tumor subtypes, 
cytogenetic abnormalities and metastasis formation.
\newblock 
Holger Sueltmann, Anja von Heydebreck, Wolfgang Huber, Ruprecht Kuner, 
Andreas Buness, Markus Vogt, Bastian Gunawan, Martin Vingron, 
Laszlo Fuezesi, and Annemarie Poustka
(Division of Molecular
Genome Analysis, German Cancer Research Center, Heidelberg).
\newblock \textit{Submitted 2004}.

\end{thebibliography}
\end{document}
