A high performance test of differential gene expression for oligonucleotide arrays

William J Lemon¹, Sandya Liyanarachchi² and Ming You¹^,2

¹Department of Surgery, 4940 Parkview Place, 10130 Wohl Clinics, Washington University in St Louis, St Louis, MI 63110, USA

²Division of Human Cancer Genetics, The Ohio State University Comprehensive Cancer Center, 420 West 12th Avenue, Columbus, OH 43210, USA

author email corresponding author email

Genome Biology 2003, 4:R67doi:10.1186/gb-2003-4-10-r67


Published:	10 September 2003

Subject areas: Bioinformatics, Genome studies

Abstract

Logit-t employs a logit-transformation for normalization followed by statistical testing at the probe-level. Using four publicly-available datasets, together providing 2,710 known positive incidences of differential expression and 2,913,813 known negative incidences, performance of statistical tests were: Logit-t provided 75% positive-predictive value, compared with 5% for Affymetrix Microarray Suite 5, 6% for dChip perfect match (PM)-only, and 9% for Robust Multi-array Analysis at the p < 0.01 threshold. Logit-t provided 70% sensitivity, Microarray Suite 5 provided 46%, dChip provided 53% and Robust Multi-array Analysis provided 63%.