Why do I get a big log fold change but small mean change in b value when plotting differential methylation?

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?

Sincerely, Christine

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