Journal
MATHEMATICAL BIOSCIENCES
Volume 176, Issue 1, Pages 35-51Publisher
ELSEVIER SCIENCE INC
DOI: 10.1016/S0025-5564(01)00107-9
Keywords
microarray; mixed model; split plot; probe
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Funding
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [P01GM045344] Funding Source: NIH RePORTER
- NIGMS NIH HHS [GM45344] Funding Source: Medline
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We outline and describe steps for a statistically rigorous approach to analyzing probe-level Affymetrix GeneChip data. The approach employs classical linear mixed models and operates on a gene-by-gene basis. Forgoing any attempts at gene presence or absence calls, the method simultaneously considers the data across all chips in an experiment. Primary output includes precise estimates of fold change (some as low as 1.1), their statistical significance, and measures of array and probe variability. The method can accommodate complex experiments involving many kinds of treatments and can test for their effects at the probe level. Furthermore, mismatch probe data can be incorporated in different ways or ignored altogether. Data from an ionizing radiation experiment on human cell lines illustrate the key concepts. (C) 2002 Published by Elsevier Science Inc.
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