Error when using qvalue function

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Error when using qvalue function

anikaM
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

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Re: Error when using qvalue function

Jim Lemon-4
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 <[hidden email]> 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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Re: Error when using qvalue function

anikaM
can you please send me command you used to install it?

On Mon, Oct 28, 2019 at 5:12 PM Jim Lemon <[hidden email]> 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 <[hidden email]> 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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Re: Error when using qvalue function

anikaM
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 <[hidden email]> wrote:

>
> can you please send me command you used to install it?
>
> On Mon, Oct 28, 2019 at 5:12 PM Jim Lemon <[hidden email]> 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 <[hidden email]> 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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Re: 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 <[hidden email]> 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
><[hidden email]> wrote:
>>
>> can you please send me command you used to install it?
>>
>> On Mon, Oct 28, 2019 at 5:12 PM Jim Lemon <[hidden email]>
>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
><[hidden email]> 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:
>
>______________________________________________
>[hidden email] 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.

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Re: Error when using qvalue function

anikaM
Again the same thing:

> require(qvalue)
> 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 6:31 PM Jeff Newmiller <[hidden email]> wrote:

>
> ... 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 <[hidden email]> 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
> ><[hidden email]> wrote:
> >>
> >> can you please send me command you used to install it?
> >>
> >> On Mon, Oct 28, 2019 at 5:12 PM Jim Lemon <[hidden email]>
> >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
> ><[hidden email]> 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:
> >
> >______________________________________________
> >[hidden email] 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.

______________________________________________
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Re: Error when using qvalue function

R help mailing list-2
In reply to this post by Jim Lemon-4
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 <[hidden email]> 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 <[hidden email]>
> 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:
>
> ______________________________________________
> [hidden email] 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]]

______________________________________________
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Re: Error when using qvalue function

anikaM
Hello,

I am am correct to assume that here:

pvals=q$META
qval_obj=qvalue(pvals) #is false discovery rate
pi1=1-qval_obj$pi0 #TPR
pi1  #TPR

pi1 represents True Positive Rate?

Thanks
Ana

On Mon, Oct 28, 2019 at 9:36 PM William Dunlap <[hidden email]> wrote:

>
> 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")$URL
> [1] "http://github.com/jdstorey/qvalue"
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
>
> On Mon, Oct 28, 2019 at 3:13 PM Jim Lemon <[hidden email]> wrote:
>>
>> Hi Ana,
>> Seems to work without error for me:
>>
>> # installed qvalue_1.26.0 from CRAN archive
>> library(qvalue)
>>  pvals<-c(6.919239e-02,1.073784e-01,1.218613e-01,1.586202e-01,
>>  1.370340e-01,3.452574e-02,2.545619e-01,1.676715e-02,8.571197e-01,
>>  8.649025e-01,1.777414e-02,6.801867e-01,6.873085e-01,
>>  1.276566e-01,5.907002e-02,2.343207e-02,2.078125e-02,6.404511e-02,
>>  3.306593e-02,9.411259e-04,1.038989e-03,4.734674e-05,
>>  3.422489e-05,5.606264e-05,6.322817e-02,1.291268e-02,3.452596e-03,
>>  1.770753e-01,3.285821e-01,2.292055e-02,5.503168e-02,
>>  6.940048e-01,3.638889e-03,6.799640e-01,1.301045e-02,6.794010e-01,
>>  2.339327e-02,1.038529e-01,3.137687e-04,2.148050e-02,
>>  1.783068e-01,1.764518e-01,6.386686e-03,1.670062e-02,3.220291e-01,
>>  5.568613e-01,8.886102e-01,5.031040e-01,3.760079e-01,
>>  6.638034e-02,9.419648e-03,5.885266e-03,1.539809e-02,5.296551e-03,
>>  2.425230e-02,5.023091e-01,4.547284e-03,1.850796e-01,
>>  9.389289e-02,6.544873e-03,3.031956e-03,7.772671e-03,9.073974e-03,
>>  9.118352e-02,4.075408e-04,6.902206e-01,6.929767e-02,
>>  1.897121e-02,6.693074e-02,1.111308e-02,1.286147e-02,4.515834e-02,
>>  8.886941e-01,8.891051e-01,3.792846e-01,5.368898e-01,
>>  2.323894e-01,3.220141e-01,7.320883e-02,9.642521e-03,6.024415e-01,
>>  2.459322e-02,2.873351e-01,8.477168e-01,1.351068e-02,
>>  1.053550e-01,4.812686e-01,1.404957e-01,9.835912e-02,4.373995e-01,
>>  8.803856e-02)
>> qval_obj=qvalue(pvals)
>> qval_obj$pi0
>> [1] 0.1981095
>> pi1=1-qval_obj$pi0
>> pi1
>> [1] 0.8018905
>>
>> Jiim
>>
>> On Tue, Oct 29, 2019 at 8:45 AM Ana Marija <[hidden email]> wrote:
>> >
>> > Hello,
>> >
>> > I am trying to calculate True Positive Rate, TPR with this procedure:
>> >
>> >     pvals=q$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:
>>
>> ______________________________________________
>> [hidden email] 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.

______________________________________________
[hidden email] 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.