# Interpretation of p-value histogram for differential methylation analysis: what can explain prevalence of large p-values?

I am conducting an analysis of methylation data for ~20k+ genes.

For n=3, I am doing a t-test for every gene to see if it has been differentially methylated after treatment. Methylation values range from [0,1].

So, in my data I have 6 rows, with a before and after row for each patient and # columns = # of genes (~20k).

Here is code for generating p-values:

for (i in 1:ncol(df))
{
alpha = c(df[c(1,3,5),i])
beta = c(df[c(2,4,6),i])