Cholesky factorization failed

[wangfan860]

Hello GENESIS Team,

I've encountered an issue with the fitNullModel function. I successfully ran fitNullModel when fitting a model with only an outcome and a covariate. However, when I attempt to include even a single Principal Component as a covariate, the function fails.

Here is the error:

Error in .local(x, ...) : 
  internal_chm_factor: Cholesky factorization failed
Calls: fitNullModel ... .computeSigmaQuantities -> chol -> chol -> .local -> .Call
In addition: Warning message:
In .local(x, ...) :
  Cholmod warning 'not positive definite' at file ../Cholesky/t_cholmod_rowfac.c, line 430
Execution halted

I'm wondering why the PCs are a problem? Are there any known compatibility issues with certain types of data or preprocessing steps that might affect the inclusion of PCs in the model?

Any insights or suggestions you could offer would be greatly appreciated. Thank you so much!!

[amstilp]

Thanks for asking. We've seen errors like that before when covariates are collinear, but I would be surprised if a PC were collinear with your other covariate. Can you give us some more information about how you're trying to run fitNullModel?

• What version of GENESIS are you running?
• What is the function call to fitNullModel? e.g., are you including a relatedness matrix or using heterogeneous residual variance?
• How did you create the covariates, PCs, and (if using) relatedness matrix?