A high performance test of differential gene expression for oligonucleotide arrays.

William J. Lemon, Sandya Liyanarachchi, Ming You

Research output: Contribution to journalArticlepeer-review

49 Scopus citations

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%.

Original languageEnglish (US)
Pages (from-to)R67
JournalGenome Biology
Volume4
Issue number10
StatePublished - 2003

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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