Table 3. Suggested score thresholds (SSTs) and corresponding quality summary statistics for cancer cell lines.
SSTs found seeking to fix or optimise certain quality statistics of the data. All SSTs are given to the nearest integer.
| Cell | SST giving
FNR=0.2 |
Achieved
FDR (at NST) (2.d.p) |
SST minimising
FDR (using BFGS) |
Achieved
FDR (using BFGS) (2.d.p) |
SST minimising
FDR (using NM) |
Achieved
FDR (using NM) (2.d.p) |
SST giving
FWER=0.05 |
|---|---|---|---|---|---|---|---|
| BLN2 | 2 | 0.74 | 22 | 0.61 | 390 | 0.48 | 15 |
| BLN3 | 5 | 0.75 | 5 | 0.78 | 432 | 0.88 | 15 |
| HT29 | 4 | 0.89 | 5 | 0.89 | 116 | 0.58 | 15 |
| KMS11 | 5 | 0.85 | 71 | 0.83 | 86 | 0.82 | 15 |
| KMS12BM | 7 | 0.84 | 5 | 0.84 | 898 | 0.29 | 15 |
| L428 | 9 | 0.78 | 5 | 0.78 | 904 | 0.57 | 15 |
| LoVo | 10 | 0.89 | 5 | 0.89 | 212 | 0.75 | 15 |
| MM1S | 7 | 0.85 | 5 | 0.85 | 238 | 0.43 | 15 |
| N16 | 3 | 0.81 | 5 | 0.81 | 138 | 0.5 | 15 |
| NT2 | 7 | 0.70 | 5 | 0.70 | 12 | 0.68 | 15 |
SST, suggested score threshold; FNR, false-negative rate; FDR, false-discovery rate; NST, normal score threshold; BFGS, Broyden–Fletcher–Goldfarb–Shanno; NM, Nelder-Mead; FWER, family-wise error rate.