title: Theoretical and experimental comparisons of gene expression indexes for oligonucleotide arrays.
abstract: BACKGROUND
  Oligonucleotide expression arrays exhibit systematic and reproducible variation produced by the multiple distinct probes used to represent a gene. Recently, a gene expression index has been proposed that explicitly models probe effects, and provides improved fits of hybridization intensity for arrays containing perfect match (PM) and mismatch (MM) probe pairs.
  
  
  RESULTS
  Here we use a combination of analytical arguments and empirical data to show directly that the estimates provided by model-based expression indexes are superior to those provided by commercial software. The improvement is greatest for genes in which probe effects vary substantially, and modeling the PM and MM intensities separately is superior to using the PM-MM differences. To empirically compare expression indexes, we designed a mixing experiment involving three groups of human fibroblast cells (serum starved, serum stimulated, and a 50:50 mixture of starved/stimulated), with six replicate HuGeneFL arrays in each group. Careful spiking of control genes provides evidence that 88-98% of the genes on the array are detectably transcribed, and that the model-based estimates can accurately detect the presence versus absence of a gene. The use of extensive replication from single RNA sources enables exploration of the technical variability of the array.
authors.affiliation: Division of Human Cancer Genetics, The Ohio State University, Columbus, Ohio, USA.
authors.forename: William J
authors.initials: WJ
authors.lastname: Lemon
authors.forename: Jeffrey J T
authors.initials: JJ
authors.lastname: Palatini
authors.forename: Ralf
authors.initials: R
authors.lastname: Krahe
authors.forename: Fred A
authors.initials: FA
authors.lastname: Wright
mesh_terms: D016477:Artifacts; D002478:Cells, Cultured; D016000:Cluster Analysis; D015342:DNA Probes; D005347:Fibroblasts / Q000502:physiology; D020869:Gene Expression Profiling / Q000379:methods* / Q000592:standards; D005786:Gene Expression Regulation / Q000235:genetics; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods* / Q000592:standards; D011786:Quality Control; D012313:RNA / Q000145:classification / Q000235:genetics*; D012015:Reference Standards; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*; D013223:Statistics as Topic
chemical_list: D015342:DNA Probes; D012313:RNA