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

[Jim Lemon]

Hi Ana,
Your minimum value in pvalR is very small and may be causing trouble.
As the qvalue package seems to be in Bioconductor, perhaps posting to
that help list would get an answer.

Jim

On Wed, Sep 25, 2019 at 1:48 AM Ana Marija <sokovic.anamarija using gmail.com> wrote:
>
> 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
>
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