TiArA: A virtual appliance for the analysis of tiling array data

Abstract

Background: Genomic tiling arrays have been described in the scientific literature since 2003, yet there is a shortage of userfriendly applications available for their analysis. Methodology/Principal Findings: Tiling Array Analyzer (TiArA) is a software program that provides a user-friendly graphical interface for the background subtraction, normalization, and summarization of data acquired through the Affymetrix tiling array platform. The background signal is empirically measured using a group of nonspecific probes with varying levels of GC content and normalization is performed to enforce a common dynamic range. Conclusions/Significance: TiArA is implemented as a standalone program for Linux systems and is available as a crossplatform virtual machine that will run under most modern operating systems using virtualization software such as Sun VirtualBox or VMware. The software is available as a Debian package or a virtual appliance at http://purl.org/NET/tiara. © 2010 Greenbaum et al.