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Case-control differences were assayed by logistic regression, with methylation levels as a continuous variable and the same adjustment used for the case-control DMR discovery and replication analyses.
Missing data are more likely to be important for MDR, which relies on a balanced case control design, but as the result was negative, it seems unlikely that the adjustment used for missing values was inadequate.
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The toolkit was first field tested on a non-sample site, and after necessary adjustments, used for the study.
All methods and adjustments used for the discovery dataset were applied for the replication analyses in addition to adjusting for study site.
Significance level was set at 0.05 with Bonferroni adjustments used (for normally distributed data); and the Least Significant Difference (LSD) in ranks was calculated if significance was achieved using the Kruskal-Wallis rank test [ 65].
ANOVA with Tukey-Kramer adjustment was used for comparisons of three different groups.
The Fisher's least significance difference test with Bonferroni's adjustment was used for multiple comparisons of phenotypic performance.
Pair-wise genotypic differences were determined by post-hoc comparison using the LSD-Test and Tukey adjustment was used for multiple comparison of means if appropriate.
The Mann-Whitney U test with Bonferroni's adjustment was used for pair-wise comparisons when the Kruskal-Wallis test is significant.
No such adjustment was used for infections with any type, oncogenic and non-oncogenic types.
Bonferroni adjustment was used for multiple comparisons (43 comparisons); therefore a p value less than 0.001 was considered statistically significant.
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