[R] Error when using qvalue function

[Jeff Newmiller]

... 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 using 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 using 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 using 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 using 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:
>
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