I encountered a message "Level 1 model did not converge" during step1. I'm seeking clarification on the potential causes behind this convergence failure, specifically whether it indicates:
-
Lack of association between genetic structure and phenotype
Does this suggest that the genetic variants included in the model do not explain significant variance in the phenotype, leading to an unstable model?
-
Quality control (QC) issues with genetic variants
Could this be a result of poor QC (e.g., high missing rate, low minor allele frequency, or excessive relatedness in samples), which introduces noise and prevents model convergence?
What are the primary factors (genetic/statistical) that cause level 1 model non-convergence?
Any insights or references to relevant documentation/studies would be greatly appreciated!
Thank you
I encountered a message "Level 1 model did not converge" during step1. I'm seeking clarification on the potential causes behind this convergence failure, specifically whether it indicates:
Lack of association between genetic structure and phenotype
Does this suggest that the genetic variants included in the model do not explain significant variance in the phenotype, leading to an unstable model?
Quality control (QC) issues with genetic variants
Could this be a result of poor QC (e.g., high missing rate, low minor allele frequency, or excessive relatedness in samples), which introduces noise and prevents model convergence?
What are the primary factors (genetic/statistical) that cause level 1 model non-convergence?
Any insights or references to relevant documentation/studies would be greatly appreciated!
Thank you