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A high performance test of differential gene expression for oligonucleotide arrays

William J Lemon1, Sandya Liyanarachchi2 and Ming You12*

Author Affiliations

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

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

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Genome Biology 2003, 4:R67  doi:10.1186/gb-2003-4-10-r67

Published: 10 September 2003

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%.