negbin.regs Hang Forever!

[xiekunwhy]

Hi,

I found that negbin.regs() in Rfast2 Hang Forever sometimes, it is a nightmare when using negbin.regs() inside a apply or for loop, I think it is a serious bug.
And the attached data can be used to reproduce the bug and to reproduce the warnings(warning: solve(): system seems singular; attempting approx solution) in this issue RfastOfficial/Rfast#48
abnormal_y.xls

The script I have used:
library(Rfast2)
exp <- read.table("abnormal_y.xls", header = T, stringsAsFactors = F)
x <- as.matrix(exp$x)

y1 <- exp[,1]
t1 <- negbin.regs(y1, x) ## end normally

y2 <- exp[,2]
t2 <- negbin.regs(y2, x) ## Hang Forever

sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] Rfast2_0.0.9 Rcpp_1.0.7

loaded via a namespace (and not attached):
[1] Rfast_2.0.3 compiler_4.1.0 RcppZiggurat_0.1.6 parallel_4.1.0
[5] tools_4.1.0 RANN_2.6.1

Best,
Kun

[xiekunwhy]

Hi Rfast developers,

I found that the problem is in negbin.mle() function, Rfast::negbin.mle(y)$loglik hang forever but Rfast::negbin.mle(y, type = 2) works well.
So would you please add an option to negbin.regs() to make it possible to choose type value?

The same problem also take place in when running score.negbinregs()

[statlink]

Can you send me the response variable data with an email to check this?
We will add this argument you just mentioned.

Michail

[xiekunwhy]

Hi Michail ,

I can not find your e-mail address, please provide one. I will send you same 10X-RNA-seq data to test multiple ys to single x.

Best,
Kun

[statlink]

mtsagris@uoc.gr