I have performed a probe wise differencial methylation analysis from a set of beta values downloaded from de TCGA. I have obtained a set of differencially methylated probes (dmp) for two groups of samples, but their log2 fold change (log2FC) range from -0.3 to 0.4. Then, I have performed exactly the same analysis, but transforming the Beta values to M values using
lumi package. Now, the log2FC range from -3 to 4.
So, looking to M values results, it seems that the effect size of the probes is quite big, but, when I look to the Beta values result, then the effect seems quite low.
So, I was thinking to filter those probes with abs (log2FC) < 1, using the results of M values, but I am worried about their low log2FC when Beta values are used. Do you think it would be okay this approach or that the better is to use the log2FC from the Beta values results (which in my case seems too low)?