Hello,
I am trying to calculate True Positive Rate, TPR with this procedure:
pvals=q$METAge
qval_obj=qvalue(pvals) #is false discovery rate
pi1=1-qval_obj$pi0 #TPR
pi1 #TPR
But I am getting this error:
Error in smooth.spline(lambda, pi0, df = smooth.df) :
missing or infinite values in inputs are not allowed
I have 91 p values and they look like this:
> pvals
[1] 6.919239e-02 1.073784e-01 1.218613e-01 1.586202e-01
1.370340e-01 3.452574e-02 2.545619e-01 1.676715e-02 8.571197e-01
[10] 8.649025e-01 1.777414e-02 6.801867e-01 6.873085e-01
1.276566e-01 5.907002e-02 2.343207e-02 2.078125e-02 6.404511e-02
[19] 3.306593e-02 9.411259e-04 1.038989e-03 4.734674e-05
3.422489e-05 5.606264e-05 6.322817e-02 1.291268e-02 3.452596e-03
[28] 1.770753e-01 3.285821e-01 2.292055e-02 5.503168e-02
6.940048e-01 3.638889e-03 6.799640e-01 1.301045e-02 6.794010e-01
[37] 2.339327e-02 1.038529e-01 3.137687e-04 2.148050e-02
1.783068e-01 1.764518e-01 6.386686e-03 1.670062e-02 3.220291e-01
[46] 5.568613e-01 8.886102e-01 5.031040e-01 3.760079e-01
6.638034e-02 9.419648e-03 5.885266e-03 1.539809e-02 5.296551e-03
[55] 2.425230e-02 5.023091e-01 4.547284e-03 1.850796e-01
9.389289e-02 6.544873e-03 3.031956e-03 7.772671e-03 9.073974e-03
[64] 9.118352e-02 4.075408e-04 6.902206e-01 6.929767e-02
1.897121e-02 6.693074e-02 1.111308e-02 1.286147e-02 4.515834e-02
[73] 8.886941e-01 8.891051e-01 3.792846e-01 5.368898e-01
2.323894e-01 3.220141e-01 7.320883e-02 9.642521e-03 6.024415e-01
[82] 2.459322e-02 2.873351e-01 8.477168e-01 1.351068e-02
1.053550e-01 4.812686e-01 1.404957e-01 9.835912e-02 4.373995e-01
[91] 8.803856e-02
Please advise,
Ana
Hi Ana, Seems to work without error for me: # installed qvalue_1.26.0 from CRAN archive library(qvalue) pvals<-c(6.919239e-02,1.073784e-01,1.218613e-01,1.586202e-01, 1.370340e-01,3.452574e-02,2.545619e-01,1.676715e-02,8.571197e-01, 8.649025e-01,1.777414e-02,6.801867e-01,6.873085e-01, 1.276566e-01,5.907002e-02,2.343207e-02,2.078125e-02,6.404511e-02, 3.306593e-02,9.411259e-04,1.038989e-03,4.734674e-05, 3.422489e-05,5.606264e-05,6.322817e-02,1.291268e-02,3.452596e-03, 1.770753e-01,3.285821e-01,2.292055e-02,5.503168e-02, 6.940048e-01,3.638889e-03,6.799640e-01,1.301045e-02,6.794010e-01, 2.339327e-02,1.038529e-01,3.137687e-04,2.148050e-02, 1.783068e-01,1.764518e-01,6.386686e-03,1.670062e-02,3.220291e-01, 5.568613e-01,8.886102e-01,5.031040e-01,3.760079e-01, 6.638034e-02,9.419648e-03,5.885266e-03,1.539809e-02,5.296551e-03, 2.425230e-02,5.023091e-01,4.547284e-03,1.850796e-01, 9.389289e-02,6.544873e-03,3.031956e-03,7.772671e-03,9.073974e-03, 9.118352e-02,4.075408e-04,6.902206e-01,6.929767e-02, 1.897121e-02,6.693074e-02,1.111308e-02,1.286147e-02,4.515834e-02, 8.886941e-01,8.891051e-01,3.792846e-01,5.368898e-01, 2.323894e-01,3.220141e-01,7.320883e-02,9.642521e-03,6.024415e-01, 2.459322e-02,2.873351e-01,8.477168e-01,1.351068e-02, 1.053550e-01,4.812686e-01,1.404957e-01,9.835912e-02,4.373995e-01, 8.803856e-02) qval_obj=qvalue(pvals) qval_obj$pi0 [1] 0.1981095 pi1=1-qval_obj$pi0 pi1 [1] 0.8018905 Jiim On Tue, Oct 29, 2019 at 8:45 AM Ana Marija <sokovic.anamarija at gmail.com> wrote:> > Hello, > > I am trying to calculate True Positive Rate, TPR with this procedure: > > pvals=q$METAge > qval_obj=qvalue(pvals) #is false discovery rate > pi1=1-qval_obj$pi0 #TPR > pi1 #TPR > > But I am getting this error: > > Error in smooth.spline(lambda, pi0, df = smooth.df) : > missing or infinite values in inputs are not allowed > > I have 91 p values and they look like this:
can you please send me command you used to install it? On Mon, Oct 28, 2019 at 5:12 PM Jim Lemon <drjimlemon at gmail.com> wrote:> > Hi Ana, > Seems to work without error for me: > > # installed qvalue_1.26.0 from CRAN archive > library(qvalue) > pvals<-c(6.919239e-02,1.073784e-01,1.218613e-01,1.586202e-01, > 1.370340e-01,3.452574e-02,2.545619e-01,1.676715e-02,8.571197e-01, > 8.649025e-01,1.777414e-02,6.801867e-01,6.873085e-01, > 1.276566e-01,5.907002e-02,2.343207e-02,2.078125e-02,6.404511e-02, > 3.306593e-02,9.411259e-04,1.038989e-03,4.734674e-05, > 3.422489e-05,5.606264e-05,6.322817e-02,1.291268e-02,3.452596e-03, > 1.770753e-01,3.285821e-01,2.292055e-02,5.503168e-02, > 6.940048e-01,3.638889e-03,6.799640e-01,1.301045e-02,6.794010e-01, > 2.339327e-02,1.038529e-01,3.137687e-04,2.148050e-02, > 1.783068e-01,1.764518e-01,6.386686e-03,1.670062e-02,3.220291e-01, > 5.568613e-01,8.886102e-01,5.031040e-01,3.760079e-01, > 6.638034e-02,9.419648e-03,5.885266e-03,1.539809e-02,5.296551e-03, > 2.425230e-02,5.023091e-01,4.547284e-03,1.850796e-01, > 9.389289e-02,6.544873e-03,3.031956e-03,7.772671e-03,9.073974e-03, > 9.118352e-02,4.075408e-04,6.902206e-01,6.929767e-02, > 1.897121e-02,6.693074e-02,1.111308e-02,1.286147e-02,4.515834e-02, > 8.886941e-01,8.891051e-01,3.792846e-01,5.368898e-01, > 2.323894e-01,3.220141e-01,7.320883e-02,9.642521e-03,6.024415e-01, > 2.459322e-02,2.873351e-01,8.477168e-01,1.351068e-02, > 1.053550e-01,4.812686e-01,1.404957e-01,9.835912e-02,4.373995e-01, > 8.803856e-02) > qval_obj=qvalue(pvals) > qval_obj$pi0 > [1] 0.1981095 > pi1=1-qval_obj$pi0 > pi1 > [1] 0.8018905 > > Jiim > > On Tue, Oct 29, 2019 at 8:45 AM Ana Marija <sokovic.anamarija at gmail.com> wrote: > > > > Hello, > > > > I am trying to calculate True Positive Rate, TPR with this procedure: > > > > pvals=q$METAge > > qval_obj=qvalue(pvals) #is false discovery rate > > pi1=1-qval_obj$pi0 #TPR > > pi1 #TPR > > > > But I am getting this error: > > > > Error in smooth.spline(lambda, pi0, df = smooth.df) : > > missing or infinite values in inputs are not allowed > > > > I have 91 p values and they look like this:
With qvalue-2.16.0 and R-3.6.1 many calls to qvalue::qvalue die in its call to qvalue::pi0est. E.g.,> trace(smooth.spline, quote(cat("y=", deparse(y), "\n")))Tracing function "smooth.spline" in package "stats" [1] "smooth.spline"> qvalue::pi0est(c(.01, .01, .06))Tracing smooth.spline(lambda, pi0, df = smooth.df) on entry y= c(NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_) Error in smooth.spline(lambda, pi0, df = smooth.df) : missing or infinite values in inputs are not allowed You should submit a bug report to> packageDescription("qvalue")$URL[1] "http://github.com/jdstorey/qvalue" Bill Dunlap TIBCO Software wdunlap tibco.com On Mon, Oct 28, 2019 at 3:13 PM Jim Lemon <drjimlemon at gmail.com> wrote:> Hi Ana, > Seems to work without error for me: > > # installed qvalue_1.26.0 from CRAN archive > library(qvalue) > pvals<-c(6.919239e-02,1.073784e-01,1.218613e-01,1.586202e-01, > 1.370340e-01,3.452574e-02,2.545619e-01,1.676715e-02,8.571197e-01, > 8.649025e-01,1.777414e-02,6.801867e-01,6.873085e-01, > 1.276566e-01,5.907002e-02,2.343207e-02,2.078125e-02,6.404511e-02, > 3.306593e-02,9.411259e-04,1.038989e-03,4.734674e-05, > 3.422489e-05,5.606264e-05,6.322817e-02,1.291268e-02,3.452596e-03, > 1.770753e-01,3.285821e-01,2.292055e-02,5.503168e-02, > 6.940048e-01,3.638889e-03,6.799640e-01,1.301045e-02,6.794010e-01, > 2.339327e-02,1.038529e-01,3.137687e-04,2.148050e-02, > 1.783068e-01,1.764518e-01,6.386686e-03,1.670062e-02,3.220291e-01, > 5.568613e-01,8.886102e-01,5.031040e-01,3.760079e-01, > 6.638034e-02,9.419648e-03,5.885266e-03,1.539809e-02,5.296551e-03, > 2.425230e-02,5.023091e-01,4.547284e-03,1.850796e-01, > 9.389289e-02,6.544873e-03,3.031956e-03,7.772671e-03,9.073974e-03, > 9.118352e-02,4.075408e-04,6.902206e-01,6.929767e-02, > 1.897121e-02,6.693074e-02,1.111308e-02,1.286147e-02,4.515834e-02, > 8.886941e-01,8.891051e-01,3.792846e-01,5.368898e-01, > 2.323894e-01,3.220141e-01,7.320883e-02,9.642521e-03,6.024415e-01, > 2.459322e-02,2.873351e-01,8.477168e-01,1.351068e-02, > 1.053550e-01,4.812686e-01,1.404957e-01,9.835912e-02,4.373995e-01, > 8.803856e-02) > qval_obj=qvalue(pvals) > qval_obj$pi0 > [1] 0.1981095 > pi1=1-qval_obj$pi0 > pi1 > [1] 0.8018905 > > Jiim > > On Tue, Oct 29, 2019 at 8:45 AM Ana Marija <sokovic.anamarija at gmail.com> > wrote: > > > > Hello, > > > > I am trying to calculate True Positive Rate, TPR with this procedure: > > > > pvals=q$METAge > > qval_obj=qvalue(pvals) #is false discovery rate > > pi1=1-qval_obj$pi0 #TPR > > pi1 #TPR > > > > But I am getting this error: > > > > Error in smooth.spline(lambda, pi0, df = smooth.df) : > > missing or infinite values in inputs are not allowed > > > > I have 91 p values and they look like this: > > ______________________________________________ > 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]]