A high performance test of differential gene expression for oligonucleotide arrays.
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%.
D000465:Algorithms; D020869:Gene Expression Profiling / Q000592:standards*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards*; D012984:Software