Sec-BiocCase.Rnw

\section{A Bioc script}

\begin{frame}
  \begin{block}{}
    A typical Bioconductor script for microarray data analysis.
    \begin{itemize}
    \item Getting data
    \item Import data into \R using dedicated infrastructure
    \item Analyse
    \item Save script, plots and objects      
    \end{itemize}
  \end{block}
\end{frame}


\begin{frame}
  \begin{block}{Using a subset of the \textit{tg-gates} data}
    \begin{itemize}
    \item \texttt{E-MTAB-800}: transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from repeat dosing studies\footnote{\url{http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-800/}}
    \item Downloaded and unzipped \texttt{E-MTAB-800.raw.1.zip}
    \item Using only a subset of files below.
    \end{itemize}     
  \end{block}
\end{frame}


\begin{frame}[fragile]{\exercise}
  \begin{block}{Loading libraries}
<<biocenv, eval = FALSE>>=
library("Biobase")
library("affy")
@     
  \end{block}    
  \begin{block}{Reading data}
<<readcel, eval = FALSE>>=
rawdata <- ReadAffy(filenames = flnms)
@     
  \end{block}
  \begin{block}{Normalisation}
<<norm, eval = FALSE>>=
eset <- rma(rawdata)
@     
  \end{block}
See \texttt{Exercise-06.R}
\end{frame}