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LAB4 (RNW)
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<h1 class="documentFirstHeading">LAB4 (RNW)</h1>
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%
<br />% NOTE -- ONLY EDIT THE .Rnw FILE!!! The .tex file is
<br />% likely to be overwritten.
<br />%
<br />% \VignetteIndexEntry{Seattle Lab 4A}
<br />%\VignetteDepends{Biobase,marrayNorm,marrayPlots}
<br />%\VignetteKeywords{Microarray}
<br />\documentclass[12pt]{article}
<br />
<br />\usepackage{amsmath,pstricks}
<br />\usepackage[authoryear,round]{natbib}
<br />\usepackage{hyperref}
<br />
<br />
<br />\textwidth=6.2in
<br />\textheight=8.5in
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<br />\bibliographystyle{plainnat}
<br />
<br />\title{Lab 4A: An Introduction to Bioconductor's {\tt marray} packages}
<br />
<br />\begin{document}
<br />
<br />\maketitle
<br />
<br />In this lab, we demonstrate the main functions in the \verb+marray+
<br />suite of packages for diagnostic plots and normalization of two-color
<br />spotted microarray data. To load the packages
<br />
<br /><<loadpacks>>=
<br />library(marrayNorm)
<br />@
<br />
<br />For a more detailed introduction, consult the package vignettes which
<br />can be listed by the command {\tt openVignette()}. A demo for
<br />\verb+marrayPlots+ can also be accessed by {\tt demo(marrayPlots)}. We
<br />will work with the sample dataset \verb+swirl+; for a description of
<br />\verb+swirl+, type {\tt ? swirl}. To load this dataset
<br />
<br /><<loaddata>>=
<br />data(swirl)
<br />@
<br />
<br />%%%%%%%%%%%%%%%%%%%%%%%%%
<br />%%% marrayClasses
<br />
<br />\section{Basic classes and methods: {\tt marrayClasses} package}
<br />
<br />One of the main classes in \verb+marrayClasses+ is the \verb+marrayLayout+
<br />class; it is used to keep track of important layout parameters, such as the total number of spotted probe sequences on the array, the dimensions of
<br /> the spot and grid matrices, the plate origin of the probes,
<br /> information on spotted control sequences.
<br />For details on this class consult the help file, {\tt ?
<br />marrayLayout. Two other important classes are
<br />\verb+marrayRaw+ and \verb+marrayNorm+, which represent, respectively,
<br />pre-normalization and post-normalization intensity data for a batch
<br /> of spotted microarrays. Methods for manipulating instances of these
<br />classes are also described in the help files.
<br />
<br />The object \verb+swirl+ is an instance of the class
<br />\verb+marrayRaw+. Try the following commands to obtain information on
<br />this object
<br />
<br /><<swirl1>>=
<br />class(swirl)
<br />slotNames(swirl)
<br />swirl
<br />@
<br />
<br />
<br />To access individual slots
<br />
<br /><<swirl2>>=
<br />
<br />maLayout(swirl)
<br />maGnames(swirl)
<br />@
<br />
<br />As with other microarray objects in Bioconductor packages, you can
<br />use subsetting commands for {\tt marrayRaw} objects
<br />
<br /><<sub>>=
<br />sw<-swirl[1:100,2]
<br />class(sw)
<br />sw
<br />@
<br />
<br />You can access red and green foreground and background intensities,
<br />and log ratios as follows
<br /><<RG>>=
<br />Gb<-maGb(swirl)
<br />dim(Gb)
<br />Gb[1:5,]
<br />Rf<-maRf(swirl)
<br />dim(Rf)
<br />Rf[1:5,]
<br />M<-maM(swirl)
<br />dim(M)
<br />@
<br />
<br />
<br />%%%%%%%%%%%%%%%%%%%%%%%%%
<br />%%% marrayInput
<br />
<br />\section{Reading in data: {\tt marrayInput} package}
<br />
<br />Functions and widgets for reading in spotted array data are
<br />provided in the \verb+marrayInput+ package, see for example {\tt ?
<br />read.marrayRaw} or {\tt ? widget.marrayRaw}.
<br />
<br />
<br />%%%%%%%%%%%%%%%%%%%%%%%%%
<br />%%% marrayPlots
<br />
<br />\section{Diagnostic plots: {\tt marrayPlots} package}
<br />
<br />The \verb+marrayPlots+ package provides functions for diagnostic plots
<br />of microarray spot statistics.
<br />
<br />To produce a spatial image of background intensities for the Cy3
<br />channel in the third array
<br /><<image1,fig=TRUE>>=
<br />tmp<-maImage(swirl[,3],x="maGb",bar=FALSE)
<br />@
<br />
<br />To produce a spatial image of log ratios for the first array in the batch
<br /><<image2,fig=TRUE>>=
<br />tmp<-maImage(swirl[,1],col=maPalette(low="blue",high="yellow"),bar=FALSE)
<br />@
<br />
<br />To produce boxplots of log ratios by sector for the first array in the batch
<br /><<boxplot1,fig=TRUE>>=
<br />maBoxplot(swirl[,1])
<br />@
<br />
<br />
<br />To produce boxplots of log ratios by plate for the second array in the batch
<br /><<boxplot2,fig=TRUE>>=
<br />maPlate(swirl)<-maCompPlate(swirl,n=384)
<br />maBoxplot(swirl[,2],x="maPlate",names=NULL)
<br />@
<br />
<br />For boxplots of log ratios for all four arrays
<br /><<boxplot3,fig=TRUE>>=
<br />maBoxplot(swirl)
<br />@
<br />
<br />
<br />%%%%%%%%%%%%%%%%%%%%%%%%%
<br />%%% marrayNorm
<br />
<br />\section{Normalization: {\tt marrayNorm} package}
<br />
<br />The \verb+marrayNorm+ package implements robust adaptive location and
<br />scale normalization procedures, which correct for different types of dye
<br />biases (e.g., intensity, spatial, plate biases).
<br />
<br />The main location and scale normalization function is
<br />\verb+maNormMain+. Simpler wrapper functions are provided in
<br />\verb+maNorm+ and \verb+maNormScale+.
<br />The function operate on objects of class \verb+marrayRaw+ (or possibly \verb+marrayNorm+, if normalization is performed in several steps) and return objects of class
<br />\verb+marrayNorm+.
<br />
<br />For within-print-tip-group loess location normalization of batch swirl
<br />
<br /><<norm>>=
<br />swirl.norm<-maNormMain(swirl)
<br />@
<br />
<br />For boxplots of post-normalization log-ratios
<br /><<boxplot4,fig=TRUE>>=
<br />maBoxplot(swirl.norm[,1])
<br />@
<br />
<br /><<boxplot5,fig=TRUE>>=
<br />maBoxplot(swirl.norm)
<br />@
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />\end{document}
<br />
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