Microarray data was quantile normalized using the LIMMA Bioconductor package. Log2 ratios were then imported into Agilent Genomics Workbench (Agilent Technologies), following which the BATMAN algorithm was used to infer the methylation statuses associated with each probe47 (link). Mean methylation states were calculated for probes within a 1,000-bp window and termed a region of interest (ROI). ROIs were then filtered to those with greater than 4 probes and mapped to autosomal chromosomes. ROIs exhibiting a standard deviation greater than 0.65 were used for subgroup assignment as described below. Comparisons between subgroups were performed using a Wilcoxon rank-sum test, and P values were corrected for multiple testing using the Benjamini–Hochberg method. For comparisons of DNA methylation and other factors in this manuscript a Wilcoxon test was used and corrected for multiple testing, such that no assumptions were made regarding the normality of the data distributions.
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Methylation Analysis of Microarray Data
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Corresponding Organization :
Other organizations : University of Toronto, German Cancer Research Center, Dartmouth College, Harvard University Press, The University of Texas MD Anderson Cancer Center, Ontario Institute for Cancer Research, GlaxoSmithKline (United Kingdom), University of Amsterdam, Amsterdam University of the Arts, University of British Columbia, Uniformed Services University of the Health Sciences, University of Utah, Catholic University of America, Stanford University, Virginia Commonwealth University, University of Warsaw, Hamilton Health Sciences, University of Michigan–Ann Arbor, Ann Arbor Center for Independent Living, University of California, San Francisco, McGill University, European Molecular Biology Laboratory
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Variable analysis
independent variables
- Methylation statuses associated with each probe
- Regions of interest (ROIs) filtered to those with greater than 4 probes and mapped to autosomal chromosomes
- ROIs exhibiting a standard deviation greater than 0.65
- DNA methylation levels
- Microarray data was quantile normalized using the LIMMA Bioconductor package
- Mean methylation states were calculated for probes within a 1,000-bp window
- Comparisons between subgroups were performed using a Wilcoxon rank-sum test, and P values were corrected for multiple testing using the Benjamini–Hochberg method
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