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Design and Analysis of Two‐Phase Experiments for Gene Expression Microarrays—Part I
Author(s) -
Jarrett Richard G.,
Ruggiero Katya
Publication year - 2008
Publication title -
biometrics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.298
H-Index - 130
eISSN - 1541-0420
pISSN - 0006-341X
DOI - 10.1111/j.1541-0420.2007.00835.x
Subject(s) - dna microarray , gene expression , microarray , gene , microarray analysis techniques , phase (matter) , computational biology , messenger rna , gene expression profiling , biology , phase variation , expression (computer science) , genetics , microbiology and biotechnology , bioinformatics , computer science , chemistry , phenotype , organic chemistry , programming language
Summary 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.