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weizhou0 / qtl

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Step 1 missing value where TRUE/FALSE needed #14

Open drneavin opened 3 months ago

drneavin commented 3 months ago

I'm receiving an error in step 1 for about half of the genes I've tested so far. Any ideas on how I might be able to resolve this? Happy to provide a more extensive log file if that's helpful as well.

Error in if (sum(tau[2:length(tau)]) == 0) { :
  missing value where TRUE/FALSE needed
Calls: fitNULLGLMM_multiV -> system.time -> glmmkin.ai_PCG_Rcpp_multiV
Timing stopped at: 5.162 0.094 5.279
Execution halted

Thanks for your help!

drneavin commented 3 months ago

I updated my the genotype file in step 1 to use just 1,000 representative SNPs as recommended in issue 12 which I thought might resolve this issue but I'm still running into a similar error to the one originally reported:

Error in if (max(abs(alpha - alpha0)/(abs(alpha) + abs(alpha0) + tol.coef)) <  : 
  missing value where TRUE/FALSE needed
Calls: fitNULLGLMM_multiV ... system.time -> glmmkin.ai_PCG_Rcpp_multiV -> Get_Coef_multiV
Timing stopped at: 0.622 0.02 0.648

This happens for ~15% of the genes (14/22 tested so far). I am working with a small dataset (~40 donors) so I'm wondering if it has to do with this small sample size or something else that I need to correct. Happy to provide more extensive outputs if helpful.

Thanks for your help!