I am trying to replicate GWAS results for 7 variants that when I perform logistic regression analysis using firth test returns NAs and works fine with linear regression. the sample sizes and MAF are not terrible because that might be reason
| Hail_linear (age, PC1-PC5) | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| SNP | N_males_afr | N_Case_afr | N_controls_afr | MAC | MAF | freq_case | freq_controls | beta | se |
| a | 3138 | 384 | 2647 | 200 | 3.19E-02 | 0.032552 | 0.003211 | -1.61E-02 | 1.08E-02 |
| b | 3138 | 384 | 2647 | 161 | 2.57E-02 | 0.023438 | 0.001511 | -5.45E-03 | 1.22E-02 |
| c | 3138 | 384 | 2647 | 117 | 1.86E-02 | 0.022135 | 0.0034 | 3.95E-02 | 1.39E-02 |
| d | 3138 | 384 | 2647 | 201 | 3.20E-02 | 0.028646 | 0.003589 | -1.87E-02 | 1.09E-02 |