randomization in laboratory procedure is key to obtaining reproducible microarray results随机化在实验室过程是获得可再生的关键芯片结果.pdfVIP

Randomization in Laboratory Procedure Is Key to Obtaining Reproducible Microarray Results 1 2 2 3 4 Hyuna Yang , Christina A. Harrington , Kristina Vartanian , Christopher D. Coldren , Rob Hall , Gary A. Churchill1* 1The Jackson Laboratory, Bar Harbor, Maine, United States of America, 2 Gene Microarray Shared Resource, OHSU Cancer Institute, Oregon Health and Science University, Portland, Oregon, United States of America, 3 Pulmonary Sciences and Critical Care Medicine University of Colorado Health Sciences Center, Denver, Colorado, United States of America, 4 Center for Array Technologies, Department of Microbiology, University of Washington, Seattle, Washington, United States of America Abstract The quality of gene expression microarray data has improved dramatically since the first arrays were introduced in the late 1990s. However, the reproducibility of data generated at multiple laboratory sites remains a matter of concern, especially for scientists who are attempting to combine and analyze data from public repositories. We have carried out a study in which a common set of RNA samples was assayed five times in four different laboratories using Affymetrix GeneChip arrays. We observed dramatic differences in the results across laboratories and identified batch effects in array processing as one of the primary causes for these differences. When batch processing of samples is confounded with experimental factors of interest it is not possible to separate their effects, and lists of differentially expressed genes may include many artifacts. This study demonstrates the substantial impact of sample processing on microarray analysis results and underscores the need for randomization in the laboratory as a means to avoid confounding of biolog