Table 3.
Genomic inflation factor λ for analyses with various control datasets
| Control:case ratio | Controls used | Controls n | Significant principal components | λ | |
|---|---|---|---|---|---|
| without PCA correction | with PCA correction | ||||
| 1:1 | MSKCC pancreatic cancer study controls | 202 | 3 | 1.009 | 1.005 |
| 5:1 | SAGE | 1,488 | 5 | 1.50 | 1.014 |
| MSKCC pancreatic cancer study controls | |||||
| 5:1 | CGEMS breast cancer | 1,344 | 6 | 1.52 | 1.018 |
| MSKCC pancreatic cancer study controls | |||||
| 5:1 | CGEMS prostate cancer | 1,350 | 5 | 1.64 | 1.019 |
| MSKCC pancreatic cancer study controls | |||||
| 5:1 | CIDR PD | 1,276 | 5 | 1.53 | 1.008 |
| MSKCC pancreatic cancer study controls | |||||
| 10:1 | SAGE | 2,522 | 7 | 1.71 | 1.015 |
| A genome-wide scan of lung cancer and smoking | |||||
| SIALS | |||||
| MSKCC pancreatic cancer study controls | |||||
| 20:1 | SAGE | 5,628 | 20 | 1.81 | 1.03 |
| A genome-wide scan of lung cancer and smoking | |||||
| CIDR PD | |||||
| SIALS | |||||
| CGEMS breast cancer | |||||
| CGEMS prostate cancer | |||||
| MSKCC pancreatic cancer study controls | |||||