Hello,
I tried using qvalue function:
library(qvalue)
qval_obj=qvalue(pvalR)
pi1=1-qval_obj$pi0
but after running:
qval_obj=qvalue(pvalR)
Error in smooth.spline(lambda, pi0, df = smooth.df) :
missing or infinite values in inputs are not allowed
or
qval_obj=qvalue(pvalR,lambda=0.5)
Error in pi0est(p, ...) :
ERROR: The estimated pi0 <= 0. Check that you have valid
p-values or use a different range of lambda.
I checked:
max(pvalR)
[1] 0.000352731
min(pvalR)
[1] 1.84872e-127
sum(is.na(pvalR))
[1] 0
sum(is.infinite(pvalR))
[1] 0
Please advise,
Thanks
Ana
https://cran.r-project.org/web/packages/qvalue/index.html states Package ?qvalue? was removed from the CRAN repository. Just an FYI On Tue, Sep 24, 2019 at 6:48 PM Ana Marija <sokovic.anamarija at gmail.com> wrote:> Hello, > > I tried using qvalue function: > > library(qvalue) > qval_obj=qvalue(pvalR) > pi1=1-qval_obj$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 at 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. >[[alternative HTML version deleted]]
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 at 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 at 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.