Additional file 20.

ANOVA models for the effect of methylation and TATA-box presence on gene responsiveness, by category of experimental treatment. The models have the form Y ~ aX + b, where X was a factor encoding the presence or absence of those features as two different levels. We used the 'aov' function in R to fit the model. The F statistic estimates the significance of the contribution of the factors to the response. The differences between the levels of the factors were estimated by the Tukey procedure, using the 'glht' function from the 'multcomp' package in R. This is equivalent to comparing the coefficients of the factors. The Bayesian Information Criteria was calculated in R using the 'BIC' function in the package 'nlme'. This parameter represents the "a posteriori" probability of the model to be true, being maximized when the magnitude of the parameter is minimized.

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Aceituno et al. BMC Genomics 2008 9:438   doi:10.1186/1471-2164-9-438