Test and document truncated p-values #18
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This describes the problem with truncated p-values causing an error in qvalue, as raised repeatedly in StoreyLab#9 and https://support.bioconductor.org/p/105623/ Hopefully, describing the problem in the help file will make it easier for users to diagnose and fix.
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This is an attempted fix of the error where if truncated p-value distributions are input with default parameters, qvalue fails with
Error in smooth.spline(lambda, pi0, df = smooth.df).This error has been raised repeatedlt, in #9, #17 and https://support.bioconductor.org/p/105623/
And I just had the same problem.
I made 2 changes to qvalue:
pnow describes this problem and how to fix itmax(p) < 0.5andpi0 = NULLThe goal is that users will encounter the error in the doucmentation and fix it quickly without needing to google.