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Bioinformatics Advance Access originally published online on July 14, 2009
Bioinformatics 2009 25(18):2425-2429; doi:10.1093/bioinformatics/btp430
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

WebArrayDB: cross-platform microarray data analysis and public data repository

Xiao-Qin Xia 1,*, Michael McClelland 1,*, Steffen Porwollik 1, Wenzhi Song 1,2, Xianling Cong 3 and Yipeng Wang 1,4,*

1Vaccine Research Institute San Diego, 10835 Road to the Cure, San Diego, CA 92121, USA, 2Department of Oralogy, 3Department of Dermatology, China Japan Union Hospital, Jilin University, Changchun, 130031, China and 4Department of Pathology & Laboratory Medicine, University of California, Irvine, CA 92697, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Cross-platform microarray analysis is an increasingly important research tool, but researchers still lack open source tools for storing, integrating and analyzing large amounts of microarray data obtained from different array platforms.

Results: An open source integrated microarray database and analysis suite, WebArrayDB (http://www.webarraydb.org), has been developed that features convenient uploading of data for storage in a MIAME (Minimal Information about a Microarray Experiment) compliant fashion, and allows data to be mined with a large variety of R-based tools, including data analysis across multiple platforms. Different methods for probe alignment, normalization and statistical analysis are included to account for systematic bias. Student's t-test, moderated t-tests, non-parametric tests and analysis of variance or covariance (ANOVA/ANCOVA) are among the choices of algorithms for differential analysis of data. Users also have the flexibility to define new factors and create new analysis models to fit complex experimental designs. All data can be queried or browsed through a web browser. The computations can be performed in parallel on symmetric multiprocessing (SMP) systems or Linux clusters.

Availability: The software package is available for the use on a public web server (http://www.webarraydb.org) or can be downloaded.

Contact: xqxia70{at}gmail.com; mcclelland.michael{at}gmail.com; yipengw{at}gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Joaquin Dopazo

Received on March 27, 2009; revised on June 9, 2009; accepted on July 5, 2009

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