Chuan Jiao1, Chunling Zhang2, Rujia Dai1, Yan Xia1, Kangli Wang1, Gina Giase3, Chao Chen1,4, Chunyu Liu1,5. 1. Center for Medical Genetics, Central South University, Changsha, Hunan 410012, PR China. 2. Department of Neurology and Physiology, SUNY Upstate Medical University, Syracuse, NY 13201, USA. 3. Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60607, USA. 4. National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, Hunan 410012, PR China. 5. Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13201, USA.
Abstract
AIM: We aimed to prove the existence of positional effects in the Illumina methylation beadchip data and to find an optimal correction method. MATERIALS & METHODS: Three HumanMethylation450, three HumanMethylation27 datasets and two EPIC datasets were analyzed. ComBat, linear regression, functional normalization and single-sample Noob were used for minimizing positional effects. The corrected results were evaluated by four methods. RESULTS: We detected 52,988 CpG loci significantly associated with sample positions, 112 remained after ComBat correction in the primary dataset. The pre- and postcorrection comparisons indicate the positional effects could alter the measured methylation values and downstream analysis results. CONCLUSION: Positional effects exist in the Illumina methylation array and may bias the analyses. Using ComBat to correct positional effects is recommended.
AIM: We aimed to prove the existence of positional effects in the Illumina methylation beadchip data and to find an optimal correction method. MATERIALS & METHODS: Three HumanMethylation450, three HumanMethylation27 datasets and two EPIC datasets were analyzed. ComBat, linear regression, functional normalization and single-sample Noob were used for minimizing positional effects. The corrected results were evaluated by four methods. RESULTS: We detected 52,988 CpG loci significantly associated with sample positions, 112 remained after ComBat correction in the primary dataset. The pre- and postcorrection comparisons indicate the positional effects could alter the measured methylation values and downstream analysis results. CONCLUSION: Positional effects exist in the Illumina methylation array and may bias the analyses. Using ComBat to correct positional effects is recommended.
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