[R] how to calculate True Positive Rate in R?

[Ana Marija]

Hello,

I tried using qvalue function:

    library(qvalue)
    qval_obj=qvalue(pvalR)
    pi1=1-qval_obj$pi0

but after running:

    qval_obj=qvalue(pvalR)
    Error in smooth.spline(lambda, pi0, df = smooth.df) :
      missing or infinite values in inputs are not allowed

or

     qval_obj=qvalue(pvalR,lambda=0.5)
    Error in pi0est(p, ...) :
      ERROR: The estimated pi0 <= 0. Check that you have valid
p-values or use a different range of lambda.

I checked:

    max(pvalR)
    [1] 0.000352731
    min(pvalR)
    [1] 1.84872e-127
    sum(is.na(pvalR))
   [1] 0
   sum(is.infinite(pvalR))
   [1] 0

Please advise,

Thanks
Ana