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D. Repsilber, A. Ziegler
Two-color Microarray Experiments. Technology and Sources of Variance
Keywords: Agilent, chip, comparative hybridization, Gene expression, microarray, technical variance
OBJECTIVES: Microarray gene expression experiments have a complex technical background. Knowledge about certain technical details is inevitable to judge alternatives for both experimental design and analysis. Here, we introduce the necessary details for the socalled two-color microarray experiments and review major sources of technical variance. METHODS: We follow the sequence of experimental steps during a typical two-color microarray gene expression experiment, stressing decisive points in the choice of technique, experimental handling and biophysical basics. We point out where technical variation is to be expected. RESULTS: Tissue storage, RNA extraction techniques, as well as the microarray hybridization represent major components of technical variance to be considered. Depending on the possibilities for access to the biomedical material under investigation, choice of amplification and labeling techniques can also be decisive to avoid additional technical variance. The two-color microarray experimental approach seeks to avoid a group of probe-level technical biases making use of the advantages of an incomplete block-design. CONCLUSIONS: It is worth to know the major sources of technical variance during the typical experimental sequence, both for choice of experimental design and techniques of molecular biology, as well as for the understanding of quality control and normalization approaches. Here, early investments pay at the levelof reduced technical variance, allowing for enhanced detection levels for the effects under investigation.
Methods of Information in Medicine, Schattauer
Print ISSN: 0026-1270
Volume: 44, 01/2005
Pages: 400 - 404