Bioconductor’s marray package: Plotting component

1 Overview This document provides a detailed discussion of the plotting functions in marray package, which is a packages for diagnostic plots of two-color spotted microarray data. This docuement provides functions for diagnostic plots of microarray spot statistics, such as boxplots, scatter–plots, and spatial color images. Examination of diagnostic plots of intensity data is important in order to identify printing, hybridization, and scanning artifacts which can lead to biased inference concerning gene expression. We encourage users to read the shorter overview quick start guide on this package given in the inst/doc directory.