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.anamar...@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 > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
