Bioconductor R Packages for Exploratory Analysis and Normalization of cDNA Microarray Data

This chapter describes a collection of four R packages for exploratory analysis and normalization of two-color cDNA microarray fluorescence intensity data. R’s object-oriented class/method mechanism is exploited to allow efficient and systematic representation and manipulation of large microarray datasets of multiple types. The marrayClasses package contains class definitions and associated methods for pre- and postnormalization intensity data for batches of arrays. The marrayInput package provides functions and tcltk widgets to automate data input and the creation of microarray-specific R objects for storing these data. Functions for diagnostic plots of microarray spot statistics, such as boxplots, scatterplots, and spatial color images, are provided in marrayPlots. Finally, the marrayNorm package implements robust adaptive location and scale normalization procedures, which correct for different types of dye biases (e.g., intensity, spatial, plate biases) and allow the use of control sequences spotted onto the array and possibly spiked into the mRNA samples. The four new packages were developed as part of the Bioconductor project, which aims more generally to produce an open-source and open-development statistical computing framework for the analysis of genomic data.