I've a bunch of 500 p-values and I want to estimate the pi0 (proportion of true H0). When using the qvalue R package, two method can be used (smoother or bootstrap). Both giving very different results :
- smoother : pi0 = 0.9913
- bootstrap : pi0 = 0.234
Here are the histogram for smoother (top) and bootstrap (bottom). Do I miss something ? Which one to use ?