File: bladderbatch.Rnw

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r-bioc-bladderbatch 1.28.0-1
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% \VignetteIndexEntry{bladderbatchTutorial}
% \VignetteKeywords{Gene expression data, batch effects}
% \VignettePackage{bladderbatch}
\documentclass[12pt]{article}
<<echo=FALSE>>=
options(width=65)
@ 
\SweaveOpts{eps=FALSE,echo=TRUE}
\usepackage{times}
\usepackage{hyperref}
\usepackage{fullpage}

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

\begin{document}
\setlength{\parskip}{1\baselineskip}
\setlength{\parindent}{0pt}
\setcounter{secnumdepth}{1} 
\title{The bladderbatch data User's Guide}
\author{Jeffrey T. Leek}
\date{Modified: October 6, 2011  Compiled: \today}
\maketitle


%\bibliographystyle{plain}
\tableofcontents



\section{Overview}


The \Rpackage{bladderbatch} package contains  gene expression data on 57 samples from a bladder cancer study \cite{dyrskjot2004aa} which have been normalized with RMA and pre-processed according to a previously defined protocol \cite{leek2010aa}. The data are in an expression set object with pData including the variables ``sample'', ``outcome'', ``batch'', and ``cancer''. The first variable is the sample number, the second variable is the outcome as defined in the original study, the third variable is a batch variable defined based on the date the microarrays were processed and the cancer variable is a simplified outcome grouping all the cancers together. The data can be accessed as follows: 

<<input>>=
library(bladderbatch)
data(bladderdata)

# Get the expression data
edata = exprs(bladderEset)

# Get the pheno data
pdata = pData(bladderEset)
@

The data in this package are used as an example data set in the \Rpackage{sva} package. 


\begin{thebibliography}{1}
\bibitem{dyrskjot2004aa} Dyrskjot, L.  and Kruhffer, M.  and Thykjaer, T.  and Marcussen, N.  and Jensen, J. L.  and Miller, K.  and Orntoft, T. F., \emph{{G}ene expression in the urinary bladder: a common carcinoma in situ gene expression signature exists disregarding histopathological classification}, Cancer Research 64:4040--4048.

\bibitem{leek2010aa} Leek JT and Scharpf R and Corrada-Bravo H and Simcha D and Langmead B and Johnson WE and Geman D and Baggerly K and Irizarry IR. (2011) \emph{Tackling the widespread and critical impact of batch effects in high-throughput data}, Nature Reviews Genetics 11:733--739.
\end{thebibliography}



\end{document}