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


BACKGROUND
The software package is available for the use on a public web server (http://www.webarraydb.org) or can be downloaded. are available at Bioinformatics online.
Xia
Xiao-Qin
XQ
Vaccine Research Institute San Diego, San Diego, CA 92121, USA. xqxia70@gmail.com
McClelland
Michael
M
Porwollik
Steffen
S
Song
Wenzhi
W
Cong
Xianling
X
Wang
Yipeng
Y
D019295:Computational Biology / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D046228:Microarray Analysis / Q000379:methods*; D012984:Software; D013223:Statistics as Topic; D014584:User-Computer Interface