%\VignetteIndexEntry{ALL data intro}
%\VignetteDepends{ALL, randomForest}
%\VignettePackage{ALL}
%
% NOTE -- ONLY EDIT THE .Rnw FILE!!!  The .tex file is
% likely to be overwritten.
%
\documentclass[12pt]{article}

\usepackage{amsmath,pstricks}
\usepackage[authoryear,round]{natbib}
\usepackage{hyperref}
\usepackage{Sweave}


\textwidth=6.2in
\textheight=8.5in
%\parskip=.3cm
\oddsidemargin=.1in
\evensidemargin=.1in
\headheight=-.3in

\newcommand{\scscst}{\scriptscriptstyle}
\newcommand{\scst}{\scriptstyle}


\newcommand{\Rfunction}[1]{{\texttt{#1}}}
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\textwidth=6.2in

\bibliographystyle{plainnat} 
 
\begin{document}
%\setkeys{Gin}{width=0.55\textwidth}

\title{Intro to ALL data for Bioc monograph}
\author{VJ Carey}
\maketitle

\section{Introduction}
This document is for authors of the Bioc monograph,
it just goes over various aspects of the ALL data.
Example analyses can be added here for illustration.

\section{Attachment and data list}
<<>>=
library(ALL)
data(ALL)
show(ALL)
@
\section{Tables and graphs for phenodata}
<<>>=
print(summary(pData(ALL)))
<<fig=TRUE>>=
hist(cvv <- apply(exprs(ALL),1,function(x)sd(x)/mean(x)))
<<>>=
ok <- cvv > .08 & cvv < .18
fALL <- ALL[ok,]
show(fALL)

allx2 <- data.frame(t(exprs(fALL)), class=ALL$BT)
@
<<>>=
library(randomForest)
rf1 <- randomForest(class~.,data=allx2)
print(rf1)

@
\end{document}
