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 wrote:
>
> With qvalue-2.16.0 and R-3.6.1 many calls to qvalu
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,
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 wrote:
>
> ... which only loads the package after you run it once. You use
... 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 hum
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 input
can you please send me command you used to install it?
On Mon, Oct 28, 2019 at 5:12 PM Jim Lemon 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
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
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
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