TY - JOUR T1 - Positional effects revealed in Illumina Methylation Array and the impact on analysis JF - bioRxiv DO - 10.1101/153858 SP - 153858 AU - Chuan Jiao AU - Chunling Zhang AU - Rujia Dai AU - Yan Xia AU - Kangli Wang AU - Gina Giase AU - Chao Chen AU - Chunyu Liu Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/06/22/153858.abstract N2 - With the evolution of rapid epigenetic research, Illumina Infinium HumanMethylation BeadChips have been widely used to study DNA methylation. However, in evaluating the accuracy of this method, we found that the commonly used Illumina HumanMethylation BeadChips are substantially affected by positional effects; the DNA sample’s location in a chip affects the measured methylation levels. We analyzed three HumanMethylation450 and three HumanMethylation27 datasets by using four methods to prove the existence of positional effects. Three datasets were analyzed further for technical replicate analysis or differential methylation CpG sites analysis. The pre- and post-correction comparisons indicate that the positional effects could alter the measured methylation values and downstream analysis results. Nevertheless, ComBat, linear regression and functional normalization could all be used to minimize such artifact. We recommend performing ComBat to correct positional effects followed by the correction of batch effects in data preprocessing as this procedure slightly outperforms the others. In addition, randomizing the sample placement should be a critical laboratory practice for using such experimental platforms. Code for our method is freely available at: https://github.com/ChuanJ/posibatch. ER -