title: Design and analysis of two-phase experiments for gene expression microarrays-part I.
abstract: Gene expression microarray experiments are intrinsically two-phase experiments. Messenger RNA (mRNA), required for the microarray experiment, must first be derived from plants or animals that are exposed to a set of treatments in a previous experiment (Phase 1). The mRNA is then used in the subsequent laboratory-based microarray experiment (Phase 2) from which gene expression is measured and ultimately analyzed. We show that obtaining a valid test for the effects of treatments on gene expression depends on the design of both the Phase 1 and Phase 2 experiments. Examples show that the multiple dye-swap design at Phase 2 is more robust than the alternating loop design in the absence of prior knowledge of the relative size of variation in the Phase 1 and Phase 2 experiments.
authors.affiliation: CSIRO Mathematical and Information Sciences, Private Bag 33, Clayton South 3169, Australia.
authors.forename: Richard G
authors.initials: RG
authors.lastname: Jarrett
authors.forename: Katya
authors.initials: K
authors.lastname: Ruggiero
mesh_terms: D000465:Algorithms; D003627:Data Interpretation, Statistical; D020869:Gene Expression Profiling / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012107:Research Design