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Bioinformatics Vol. 18 no. 11 2002
Pages 1540-1541
© 2002 Oxford University Press

Applications Note

SNOMAD (Standardization and NOrmalization of MicroArray Data): web-accessible gene expression data analysis

Carlo Colantuoni 1,2,3, George Henry 1,{dagger}, Scott Zeger 3 and Jonathan Pevsner 1,2,*

1 Department of Neurology, Kennedy Krieger Institute, 707 North Broadway, Baltimore, MD 21205, USA
2 Department of Neuroscience, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
3 Department of Biostatistics, Johns Hopkins School of Public Health, Baltimore, MD 21205, USA

Received on September 11, 2001 ; revised on February 18, 2002 ; accepted on April 25, 2002

Summary: SNOMAD is a collection of algorithms for the normalization and standardization of gene expression datasets derived from diverse biological and technological sources. In addition to conventional transformations and visualization tools, SNOMAD includes two non-linear transformations which correct for bias and variance which are non-uniformly distributed across the range of microarray element signal intensities: (1) Local mean normalization; and (2) Local variance correction (Z-score generation using a locally calculated standard deviation).

Availability: The SNOMAD tools were developed in the R statistical language http://www.r-project.org/. SNOMAD is an interactive, user-friendly web-application which can be accessed freely via the internet with any standard HTML browser: http://pevsnerlab.kennedykrieger.org/snomad.htm.

Contact: ccolantu{at}jhmi.edu or pevsner{at}jhmi.edu

* To whom correspondence should be addressed.

{dagger} Present address: Wadham College, Oxford University, UK.


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