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Filtering out probes with potential errors and adjusting experimental bias have been necessary data pre-processing steps. There is also ‘positional effects’ that the same sample in different physical positions on the array could be measured as different methylation levels. The earliest mention of the positional effect in the Illumina gene expression microarray analysis did not provide a method for correction except an advisement to randomly set the samples in the array (Verdugo et al., 2009).
(Verdugo et al., 2009) Importance of randomization in microarray experimental designs with Illumina platforms. Nucleic Acids Res.
(Jiao et al., 2017) Positional effects revealed in Illumina Methylation Array and the impact on analysis. bioRxiv.