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,
HI Rui,
thank you so much for this. I tried with the sqldf but it didn't help.
Next I tried your 2nd method and I was following your steps until:
> res2 <- asign[i2, setdiff(names(asign), names(l4))]
> m=merge(res, res2, by.x = c("chr", "pos"), by.y = c("chr", "pos"))
Error in
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
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
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,
>
On 10/28/19 2:17 PM, varin sacha via R-help wrote:
Dear R-experts,
My reproducible example here below is not working because of an error message :
Erreur : vecteurs de mémoire épuisés (limite atteinte ?)
My code perfectly works when n=3000 or n=5000 but as soon as n=1 my code
does not
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,
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
No loops necessary. Use array indexing (see ?"[", of course -- the section
on matrices and arrays)
set.seed(123)
A <- matrix(sample(1:10), nrow = 5)
B <- matrix(c(sample(1:5), sample(1:5)), nrow =5, byrow = FALSE)
## The following could be a 1-liner, but I broke it out for clarity.
ix <-
Dear R-experts,
My reproducible example here below is not working because of an error message :
Erreur : vecteurs de mémoire épuisés (limite atteinte ?)
My code perfectly works when n=3000 or n=5000 but as soon as n=1 my code
does not work anymore. By the way, my code takes a very long time
Hi Jinsong,
In such a case I think explicit loop IS the most elegant solution.
for(i in 1:2) A[,i] <- A[,i][B[,i]]
Linus
On Fri, 11 Oct 2019 at 11:44, Jinsong Zhao wrote:
>
> Hi there,
>
> I have two matrices, A and B. The columns of B is the index of the
> corresponding columns of A. I hope
Hi Michael,
I tried what you proposed with my data frame q:
> head(q)
IDP G E
wb wg we
1: rs1029830 0.0979931 0.0054060 0.39160 580.6436 40.6325 35.39774
2: rs1029832 0.1501820 0.0028140 0.39320 580.6436 40.6325 35.39774
Otra alternativa de resolución solo con la paquetería estándar:
rm(list = ls() )
## Tenemos un marco de 100 posibles participante
## que numeramos con un ID del 1 al 100 (su DNI en el estudio)
## Se asigna sexo aleatoriamente con una probablidad de 0.5 para
cada uno
marco <-
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