Guidance for DNA methylation studies: statistical insights from the Illumina EPIC array.

As linear regression is considered robust to violations of the assumptions, we next explored whether sites that violated an assumption were more likely to be significant in a DNAm analysis using a linear regression model.

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We observed no association between p -values from the gvlma tests and a DNAm site’s mean rank indicating that even highly significant rejections of the assumptions of linear regression do not bias EWAS results in terms of either false positives or false negatives (Fig. 6 ; Additional file 1 : Figure S10; Additional file 2 : Table S6).

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