TiArA: a virtual appliance for the analysis of Tiling Array data.
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.
Greenbaum
Jason A
JA
Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America. jgbaum@liai.org
Assarsson
Erika
E
Chung
Jo L
JL
Head
Steven
S
Sette
Alessandro
A
Peters
Bjoern
B
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