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\title{The bladderbatch data User's Guide}
\author{Jeffrey T. Leek}
\date{Modified: October 6, 2011  Compiled: \today}
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\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}



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