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\title{The \Bioconductor{} Project}
\author{Martin Morgan \\ Fred Hutchinson Cancer Research Center}
\date{19-21 January, 2011}

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\section{Bioconductor}

\begin{frame}{\Bioconductor{}: Analysis and Comprehension of High Throughput Genetic Data}
  \begin{description}
  \item[Goal] Help biologists understand their data
  \item[Focus]
    \begin{itemize}
    \item Expression and other microarray; flow cytometry
    \item High-throughput sequencing
    \end{itemize}
  \item[Themes]
    \begin{itemize}
    \item Open source / open development
    \item Code reuse -- statistics, visualization, domain-specific
      applications, e.g., \Biocpkg{limma}
    \item Interoperability
    \item Reproducible -- scripts, \emph{vignettes}, packages
    \end{itemize}
  \item[Success] $>400$ packages; very active mailing list; annual
    conferences (BioC2011, Seattle, July 27-29); courses; \ldots
  \end{description}
\end{frame}

\begin{frame}{The \Bioconductor{} Web Site}
  \begin{itemize}
  \item Finding and installing packages
  \item Work flows
  \item Finding help -- in and outside \R{}
  \item The \Bioconductor{} release schedule
  \item Developer support
  \item Courses and conferences
  \end{itemize}
\end{frame}

\section{Microarray Analysis}

\begin{frame}[fragile]{Work Flow: Expression Microarrays}
  Prior to analysis
  \begin{itemize}
  \item Biological experimental design -- treatments, replication,
    etc.
  \item Microarray preparation -- especially two-channel
  \end{itemize}
  Analysis
  \begin{enumerate}
  \item Pre-processing (normalization); quality assessment;
    exploratory analysis
  \item Differential expression; machine learning (clustering and
    classification)
  \item Annotation
  \item Gene set enrichment; systems biology
  \item \ldots
  \end{enumerate}
  \url{http://bioconductor.org/workflows} for common analyses.
\end{frame}

\begin{frame}{Example Data}
  Chiaretti et al., 2005~\cite{pmid16243790}
  \begin{itemize}
  \item 128 adult patients, newly diagnosed for ALL
  \item B- and T-lineage; various molecular and cytological
    characteristics.
  \item HG-U95Av2
  \item Pre-processed (background correction, normalization,
    summarization into probe sets).
  \end{itemize}
\end{frame}

\begin{frame}[fragile]{The ALL dataset}
<<load ALL package>>=
library(ALL); data(ALL); ALL
@ 
\end{frame}

\begin{frame}{Representative Packages (Microarrays)}
  \begin{description}
  \item [Pre-processing] \Biocpkg{affy}, \Biocpkg{oligo},
    \Biocpkg{lumi}, \Biocpkg{beadarray}, \Biocpkg{limma},
    \Biocpkg{genefilter}, \ldots
  \item [Machine learning] \Biocpkg{MLInterfaces}, \Biocpkg{CMA}
  \item [Differential expression] \Biocpkg{limma}, \ldots
  \item [Gene set enrichment] \Biocpkg{topGO}, \Biocpkg{GOstats},
    \Biocpkg{GSEABase}, \ldots
  \item [Annotation] \Biocpkg{AnnotationDbi}, `chip', `org' and
    \Biocpkg{BSgenome} packages
  \item [`Domain-specific'] \Biocpkg{DNAcopy}, \Biocpkg{snpMatrix},
    \ldots
  \end{description}
\end{frame}


\section{Lab activity}

\begin{frame}{Lab activity}
  Goal: learn to work with S4 classes, especially
  \Rclass{ExpressionSet}
  \begin{enumerate}
  \item Load and explore \Robject{ALL} object, including finding help
    on S4 objects.
  \item Extract \Rcode{mol.biol} \Rfunction{phenoData}, subset samples
    to include only BCR/ABL or NEG.
  \item Filter (remove) probes without gene-level annotation
  \end{enumerate}
\end{frame}

\section{References}

\begin{frame}{References}
  \bibliographystyle{plain}
  \bibliography{IWB2011}
\end{frame}

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