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 |
# Significant
Interactions at NST |
# Significant
Interactions at SST using FWER |
|---|---|---|---|---|---|---|---|---|---|
| BLN2 | 2 | 0.74 | 22 | 0.61 | 390 | 0.48 | 15 | 144678 | 34735 |
| BLN3 | 5 | 0.75 | 5 | 0.78 | 432 | 0.88 | 15 | 129017 | 13682 |
| HT29 | 4 | 0.89 | 5 | 0.89 | 116 | 0.58 | 15 | 118962 | 8959 |
| KMS11 | 5 | 0.85 | 71 | 0.83 | 86 | 0.82 | 15 | 164518 | 19290 |
| KMS12BM | 7 | 0.84 | 5 | 0.84 | 898 | 0.29 | 15 | 142163 | 14040 |
| L428 | 9 | 0.78 | 5 | 0.78 | 904 | 0.57 | 15 | 187197 | 22587 |
| LoVo | 10 | 0.89 | 5 | 0.89 | 212 | 0.75 | 15 | 95508 | 5052 |
| MM1S | 7 | 0.85 | 5 | 0.85 | 238 | 0.43 | 15 | 127784 | 9961 |
| N16 | 3 | 0.81 | 5 | 0.81 | 138 | 0.5 | 15 | 105365 | 5625 |
| NT2 | 7 | 0.70 | 5 | 0.70 | 12 | 0.68 | 15 | 174795 | 12602 |
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.