A high performance test of differential gene expression for oligonucleotide arrays
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
Genome Biology 2003, 4:R67 doi:10.1186/gb-2003-4-10-r67Published: 10 September 2003
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%.