title: A flexible two-stage procedure for identifying gene sets that are differentially expressed.
abstract: BACKGROUND
  Microarray data analysis has expanded from testing individual genes for differential expression to testing gene sets for differential expression. The tests at the gene set level may focus on multivariate expression changes or on the differential expression of at least one gene in the gene set. These tests may be powerful at detecting subtle changes in expression, but findings at the gene set level need to be examined further to understand whether they are informative and if so how.
  
  
  RESULTS
  We propose to first test for differential expression at the gene set level but then proceed to test for differential expression of individual genes within discovered gene sets. We introduce the overall false discovery rate (OFDR) as an appropriate error rate to control when testing multiple gene sets and genes. We illustrate the advantage of this procedure over procedures that only test gene sets or individual genes.
authors.affiliation: Department of Statistics, Wharton School, University of Pennsylvania, Philadelphia, PA 19104-6340, USA. ruheller@whatron.upenn.edu
authors.forename: Ruth
authors.initials: R
authors.lastname: Heller
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Manduchi
authors.forename: Gregory R
authors.initials: GR
authors.lastname: Grant
authors.forename: Warren J
authors.initials: WJ
authors.lastname: Ewens
mesh_terms: D003198:Computer Simulation; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods*; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods