title: Local false discovery rate facilitates comparison of different microarray experiments.
abstract: The local false discovery rate (LFDR) estimates the probability of falsely identifying specific genes with changes in expression. In computer simulations, LFDR <10% successfully identified genes with changes in expression, while LFDR >90% identified genes without changes. We used LFDR to compare different microarray experiments quantitatively: (i) Venn diagrams of genes with and without changes in expression, (ii) scatter plots of the genes, (iii) correlation coefficients in the scatter plots and (iv) distributions of gene function. To illustrate, we compared three methods for pre-processing microarray data. Correlations between methods were high (r = 0.84-0.92). However, responses were often different in magnitude, and sometimes discordant, even though the methods used the same raw data. LFDR complements functional assessments like gene set enrichment analysis. To illustrate, we compared responses to ultraviolet radiation (UV), ionizing radiation (IR) and tobacco smoke. Compared to unresponsive genes, genes responsive to both UV and IR were enriched for cell cycle, mitosis, and DNA repair functions. Genes responsive to UV but not IR were depleted for cell adhesion functions. Genes responsive to tobacco smoke were enriched for detoxification functions. Thus, LFDR reveals differences and similarities among experiments.
authors.affiliation: Department of Medicine, Department of Biochemistry, Department of Statistics and Health Research and Policy, Stanford University Medical Center, Stanford, CA 94305, USA.
authors.forename: Wan-Jen
authors.initials: WJ
authors.lastname: Hong
authors.forename: Robert
authors.initials: R
authors.lastname: Tibshirani
authors.forename: Gilbert
authors.initials: G
authors.lastname: Chu
mesh_terms: D002460:Cell Line; D003198:Computer Simulation; D015870:Gene Expression / Q000528:radiation effects; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011839:Radiation, Ionizing; D012907:Smoking; D014466:Ultraviolet Rays