Table 1 Comparison of ploidy prediction for ACT samples. Ploidy prediction based on scAbsolute, Ginkgo, HMMCopy, and CHISEL. Ploidy estimate is based on FACS sorting cells using DAPI staining. We considered an estimate to be an outlier if it fell outside of a \(\pm 0.5\) window around the experimental ploidy point estimate. We also gave the mean of the absolute distance in ploidy between the experimental point estimate and the computational estimate across all cells in parenthesis. The data were all sequenced with the same technology (ACT) and published in [35]. N indicates the number of cells per sample. The last row gives the mean % of outliers across all samples per method
From: scAbsolute: measuring single-cell ploidy and replication status
Sample | Ploidy | N | HMMCopy | Ginkgo | CHISEL | scAbsolute |
|---|---|---|---|---|---|---|
| Â | Â | Â | % outlier (mean distance) | |||
BT-20 | 2.70 | 1228 | 13.4 (0.51) | 1.1 (0.28) | 8.1 (0.14) | 0.5 (0.14) |
MB-157 | 2.55 | 1210 | 31.2 (0.91) | 0.5 (0.18) | 2.1 (0.16) | 0.8 (0.13) |
MB-231 | 2.41 | 897 | 34.4 (0.92) | 7.1 (0.36) | 0.1 (0.14) | 0.7 (0.05) |
MB-453 | 4.17 | 1260 | 8.1 (0.26) | 65.6 (1.06) | 42.6 (0.98) | 11.3 (0.33) |
TN1 | 3.45 | 1100 | 1.7 (0.22) | 1.8 (0.18) | 5.7 (0.21) | 0.8 (0.08) |
TN2 | 3.03 | 1024 | 3.8 (0.24) | 0.8 (0.15) | 2.6 (0.20) | 1.1 (0.10) |
TN3 | 3.44 | 1101 | 27.2 (0.92) | 2.4 (0.20) | 3.2 (0.11) | 4.5 (0.16) |
TN4 | 3.76 | 1307 | 19.8 (0.59) | 53.9 (1.18) | 47.0 (0.91) | 16.6 (0.40) |
TN5 | 2.65 | 1238 | 40.1 (1.01) | 10.9 (0.34) | 6.2 (0.19) | 18.3 (0.50) |
TN6 | 3.17 | 1060 | 2.9 (0.33) | 58.6 (0.84) | 0.0 (0.06) | 1.5 (0.12) |
TN7 | 3.15 | 605 | 4.3 (0.30) | 49.3 (1.30) | 5.1 (0.16) | 3.8 (0.16) |
TN8 | 3.95 | 1224 | 2.4 (0.33) | 69.4 (0.88) | 6.1 (0.21) | 3.0 (0.14) |
Mean % outlier | 15.8 | 26.8 | 10.7 | 5.2 | ||