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:
I did
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("qvalue")
and after entering that p value I am still getting:
> qval_obj=qvalue(pvals)
Error in smooth.spline(lambda, pi0, df = smooth.df) :
missing or infinite values in inputs are not allowed
On Mon, Oct 28, 2019 at 6:02 PM Ana Marija <sokovic.anamarija at
gmail.com> wrote:>
> 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:
... which only loads the package after you run it once. You use `require`, which fails if the package is not loaded, at which point it installs it but never runs `require` or `library` before proceeding. YMMV but I am not a fan of using `require`... getting packages installed often requires human intervention, so I prefer not to install packages in my script but just to use `library` and manually get each of the packages that `library` complains about onto my machine. Once done, the script runs just fine after that. On October 28, 2019 4:08:03 PM PDT, Ana Marija <sokovic.anamarija at gmail.com> wrote:>I did > >if (!requireNamespace("BiocManager", quietly = TRUE)) > install.packages("BiocManager") > >BiocManager::install("qvalue") > >and after entering that p value I am still getting: > >> qval_obj=qvalue(pvals) >Error in smooth.spline(lambda, pi0, df = smooth.df) : > missing or infinite values in inputs are not allowed > >On Mon, Oct 28, 2019 at 6:02 PM Ana Marija ><sokovic.anamarija at gmail.com> wrote: >> >> 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: > >______________________________________________ >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.-- Sent from my phone. Please excuse my brevity.