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Table 2 Analysis of variance of variance

From: Aging effects on DNA methylation modules in human brain and blood tissue

Source of variation, total proportion of variance explained = 15.8% logPvalue Stouffer, total proportion of variance explained = 6.7%
Source Degrees of freedom Sums of Sq Proportion of total variance F statistic P-value (F-test) Sums of Sq Proportion of total variance P-value (F-test)
PCG (Suz12+Eed+H3K27me3) OccupancyCount 1 49.35 0.071 2013.0 < 2.2E-16 82,530 0.050 < 2.2E-16
CPG_Island 2 50.78 0.073 1035.7 < 2.2E-16 24,867 0.015 < 2.2E-16
X chromosome 1 9.74 0.014 397.4 < 2.2E-16 764 0.000 5.5E-04
Distance to TSS 1 3.50E-01 0.001 14.1 1.7E-04 1,827 0.001 9.3E-08
Residual error 23,903 586.02 0.842    1,529,855 0.933  
Total variation   696.24     1,639,843   
  1. The first six columns detail the sources of variation on ave.kME with respect to the green (aging) module. Polycomb group occupancy count explains the highest proportion of the total variance followed by CpG island status (inside, outside, and shore). Comparing the results from ANOVA applied to average kME with those from applying it to the logP-value (significance measure resulting from Stouffer's meta-analysis) reveals marked differences in the proportion of variance explained (15.8% versus 6.7%), which suggests again that the average kME measure is biologically more meaningful than the meta-analysis P-value. TSS, transcription start site.