title: 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 user-friendly applications available for their analysis.
  
  
  RESULTS
  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
  TiArA is implemented as a standalone program for Linux systems and is available as a cross-platform 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.
authors.affiliation: Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America. jgbaum@liai.org
authors.forename: Jason A
authors.initials: JA
authors.lastname: Greenbaum
authors.forename: Erika
authors.initials: E
authors.lastname: Assarsson
authors.forename: Jo L
authors.initials: JL
authors.lastname: Chung
authors.forename: Steven
authors.initials: S
authors.lastname: Head
authors.forename: Alessandro
authors.initials: A
authors.lastname: Sette
authors.forename: Bjoern
authors.initials: B
authors.lastname: Peters
mesh_terms: D000465:Algorithms; D001482:Base Composition; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012815:Signal Processing, Computer-Assisted; D012984:Software; D014584:User-Computer Interface