Pvalue shows "-nan" in output of gene level association test

[ppjeep]

Most of gene-level outputs are reasonable, but there are a few lines show "-nan" in Pvalue.

Gene RANGE N_IN--geneFile ${geneF} --kernel skato
FORMATIVE NumVar NumPolyVar Q rho Pvalue
ILF2 1:153634513-153643479 8493 8 8 4027.77 0.8 -nan
DNAJB11 3:186288466-186303589 8493 3 3 591.324 0 -nan

[zhanxw]

There must be some numeric issues. Will you help provide some example data sets so that I can replicate these errors?

[suraj86nong]

Hi, I had encountered a similar problem of "-nan" in pvalue while running the SKAT. For the same, the burden test and single variant analysis were properly run. SKATO gave "NA" result. Here, I have attached an example. Kindly help me to understand and solve this problem.
Thank you.

#SKAT result
Range RANGE N_INFORMATIVE NumVar NumPolyVar Q Pvalue NumPerm ActualPerm Stat NumGreater NumEqual PermPvalue
TMEM67 8:93758521-93793294 2992 6 3 0 -nan 10000 1000 0 0 1000 0.5

#SKATO result
Range RANGE N_INFORMATIVE NumVar NumPolyVar Q rho Pvalue
TMEM67 8:93758521-93793294 2992 6 3 NA NA NA

#Single variant result
CHROM POS REF ALT N_INFORMATIVE AF INFORMATIVE_ALT_AC CALL_RATE HWE_PVALUE N_REF N_HET N_ALT U_STAT SQRT_V_STAT ALT_EFFSIZE PVALUE
8 93765617 A T 2992 0.000501337 3 1 1 2989 3 0 5.75725 1.73618 1.90997 0.000913009
8 93765648 T G 2992 0.000335121 2.00536 1 1 2990 2 0 -4.37543 1.41782 -2.1766 0.00202849
8 93793294 C T 2992 0.000167112 1 1 1 2991 1 0 -0.688028 1.00272 -0.684302 0.492611

#Burden result
Range RANGE N_INFORMATIVE NumVar NumPolyVar NonRefSite Pvalue
TMEM67 8:93758521-93793294 2992 6 3 6 0.718514

nan_results_skat_rvtests.txt

[zofieLin]

Hi, is there any updates on this issue, I also encountered a similar problem, and got a lot of "-nan" in Pvalue when doing gene-based burden test like CMC and also SKAT.

Thanks!