Randomization in Laboratory Procedure Is Key to Obtaining Reproducible Microarray Results Export

@article{citeulike:3514588, 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 biological factors with procedural effects.}, author = {Yang, Hyuna and Harrington, Christina A. and Vartanian, Kristina and Coldren, Christopher D. and Hall, Rob and Churchill, Gary A.}, citeulike-article-id = {3514588}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0003724}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19009020}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19009020}, day = {14}, doi = {10.1371/journal.pone.0003724}, journal = {PLoS ONE}, keywords = {batch-effect, experiment\_design, inter-laboratory, quality\_control, randomization, reproducible\_research}, month = {November}, number = {11}, pages = {e3724+}, posted-at = {2009-03-18 15:50:45}, priority = {3}, publisher = {Public Library of Science}, title = {Randomization in Laboratory Procedure Is Key to Obtaining Reproducible Microarray Results}, url = {http://dx.doi.org/10.1371/journal.pone.0003724}, volume = {3}, year = {2008} }

TY - JOUR ID - citeulike:3514588 L3 - citeulike-article-id:3514588 N2 - 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 biological factors with procedural effects. IS - 11 JF - PLoS ONE TI - Randomization in Laboratory Procedure Is Key to Obtaining Reproducible Microarray Results PB - Public Library of Science VL - 3 SP - e3724 KW - batch-effect KW - experiment_design KW - inter-laboratory KW - quality_control KW - randomization KW - reproducible_research AU - Yang, Hyuna AU - Harrington, Christina AU - Vartanian, Kristina AU - Coldren, Christopher AU - Hall, Rob AU - Churchill, Gary PY - 2008/11/14/ UR - http://dx.doi.org/10.1371/journal.pone.0003724 ER -