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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 ?

Thanks

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