Hello I am doing differential methylation analysis using limma. I use the m values for testing and b values for plotting. I plotted a volcano plot visualizing the p value and effect size, however I noticed something that I can't explain. Using the p value and the log fold change as reported by topTable() in limma, i get this volcano plot, which looks fairly like expected:
Volcano plot by adjusted p value and log fold change
But then I then I thought it would make more biological sense to plot the significant probes by mean differences in b value, but the significant probes seems to have really small changes in mean b value, while the nonsignificant ones have bigger changes in mean b value.
Volcano plot by adjusted p value and mean difference in b value (the axis label is wrong)
Could you help me decipher how to interpret this? I am afraid I am doing something wrong in my analysis, but I also suspect this has something to do with the calculation of b values to m values and maybe the variance. It also seems really strange that there is an inverse relationship between the p value and the mean difference in b value?