\documentclass{beamer}
\usepackage{hyperref}

\begin{document}
\title{Microarray analysis of oral cancer samples}
\author{Humberto Ortiz-Zuazaga}
\date{April 27, 2011}

\begin{frame}
\titlepage
\end{frame}

\section{Introduction}

\begin{frame}{Bioconductor}
  \begin{itemize}
  \item Bioconductor \url{http://bioconductor.org/}
  \item Software suite for analysis
of biological data
\item emphasis on microarray and other
high-throughput datasets
  \end{itemize}
\end{frame}

\begin{frame}[fragile]{Loading packages}
  Load the \verb@affy@ and \verb@limma@ packages.
<<>>=
library(limma)
library(affy)
@ 
\end{frame}


\section{Reading the data}

\begin{frame}[fragile]{Targets file}
  
A simple text file with tab separated columns can describe the
microarray samples.
<<>>=
targets <- readTargets("targets.txt")
targets
@ 
\end{frame}

\begin{frame}[fragile]{Reading the data}
<<read>>=
ab <- ReadAffy(filenames=targets$FileName)
@
\end{frame}

\section{Normalization and pre-processing}

\begin{frame}[fragile]{Normalization and summarization}
<<>>=
probeNames(ab)[1:10]

eset <- rma(ab)

featureNames(eset)[1:10]
@
\end{frame}

\begin{frame}[fragile]{Boxplot before normalization}
<<label=boxplotab,include=FALSE>>=
boxplot(ab)
@ 
<<label=figbpab,fig=TRUE,echo=FALSE>>= 
<<boxplotab>> 
@ 
\end{frame}

\begin{frame}[fragile]{Boxplot after normalization}
<<label=boxplotes,include=FALSE>>=
boxplot(exprs(eset))
@ 
<<label=figbpes,fig=TRUE,echo=FALSE>>= 
<<boxplotes>> 
@ 
\end{frame}

\section{Experimental design}

\begin{frame}[fragile]{Describing the design}
<<design>>=
f <- factor(targets$Target, levels=c("pos", "neg"))
design <- model.matrix(~0+f)
colnames(design) <- c("pos", "neg")
design
@
\end{frame}

\begin{frame}[fragile]{Fitting a model}
<<fit>>=
cont.matrix <- makeContrasts(posvsneg=pos-neg, levels=design)

fit <- lmFit(eset, design)
fit2 <- contrasts.fit(fit, cont.matrix)
fit.b <- eBayes(fit2)
@ 
\end{frame}

\section{Reporting results}

\begin{frame}[fragile]{MA plot of model fit}
<<label=maplot,include=FALSE>>=
plotMA(fit.b)
@ 
<<label=figmaplot,fig=TRUE,echo=FALSE>>= 
<<maplot>> 
@ 
\end{frame}

\begin{frame}[fragile]{Volcano plot of model fit}
<<label=volcanoplot,include=FALSE>>=
volcanoplot(fit.b)
@ 
<<label=figvolcano,fig=TRUE,echo=FALSE>>= 
<<volcanoplot>> 
@ 
\end{frame}

\begin{frame}{References}
  \begin{thebibliography}{}

\bibitem{affy}
  Gautier, L., Cope, L., Bolstad, B. M., and Irizarry, R. A. (2004).
  affy---analysis of Affymetrix GeneChip data at the probe level.
  \textit{Bioinformatics} 20, 3 (Feb. 2004), 307-315.

\bibitem{bioconductor}
R. Gentleman, V. J. Carey, D. M. Bates, B.Bolstad, M.
  Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, and others 
    Bioconductor: Open software development for computational biology and
  bioinformatics (2004).
  \textit{Genome Biology}, Vol. 5, R80

\bibitem{limma}
  Smyth, G. K. (2005). Limma: linear models for microarray data. In:
  'Bioinformatics and Computational Biology Solutions using R and
  Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W.
  Huber (eds), Springer, New York, pages 397--420.
  
\end{thebibliography}

\end{frame}
\end{document}