Genome Biology

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Software and methods for oligonucleotide and cDNA array data analysis

Matthew A Zapala, Daniel J Lockhart, Daniel G Pankratz, Anthony J Garcia, Carrolee Barlow and David J Lockhart*

Author Affiliations

The Salk Institute for Biological Studies, Laboratory of Genetics, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA

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Genome Biology 2002, 3:software0001-software0001.9 doi:10.1186/gb-2002-3-6-software0001

Published: 23 May 2002

Abstract

Two HTML-based programs were developed to analyze and filter gene-expression data: 'Bullfrog' for Affymetrix oligonucleotide arrays and 'Spot' for custom cDNA arrays. The programs provide intuitive data-filtering tools through an easy-to-use interface. A background subtraction and normalization program for cDNA arrays was also built that provides an informative summary report with data-quality assessments. These programs are freeware to aid in the analysis of gene-expression results and facilitate the search for genes responsible for interesting biological processes and phenotypes.