Table 1.
Model comparisons based on BIC and AUROC for differential methylation between (A) colon tumor and normal, (B) mutant and wildtype.
| (A) CHARM array: Tumor vs Normal | ||||||
|---|---|---|---|---|---|---|
|
| ||||||
| Model | Gaussian Mix | Kernel | Symmetric Kernel | |||
|
| ||||||
| BIC | ROC | BIC | ROC | BIC | ROC | |
| Indep | 6255209 | 0.736 | 6253765 | 0.762 | 6267078 | 0.798 |
| HMM | 6034529 | 0.589 | 6032994 | 0.609 | 6115280 | 0.935 |
| NHMM: Annot | 6033897 | 0.572 | 6038521 | 0.620 | 6114225 | 0.935 |
| NHMM: Dist | 6030418 | 0.585 | 6036719 | 0.620 | 6116526 | 0.923 |
| NHMM: CpG | 6033151 | 0.591 | 6031488 | 0.610 | 6113411 | 0.936 |
| NHMM: GC | 6031330 | 0.571 | 6027941 | 0.612 | 6111181 | 0.936 |
| NHMM: Dist+Annot | 6036219 | 0.593 | 6059388 | 0.626 | 6154113 | 0.867 |
| NHMM: Dist+CpG | 6029085 | 0.585 | 6077415 | 0.669 | 6128384 | 0.902 |
| NHMM: Dist+GC | 6027936 | 0.571 | 6037543 | 0.622 | 6115147 | 0.922 |
|
| ||||||
| BH | 0.823 | |||||
| locfdr | 0.763 | |||||
| (B) Infinium 450K array: Mutant vs Wildtype
| |||
|---|---|---|---|
| Model | Gaussian Mix | Kernel | Symmetric Kernel |
|
| |||
| BIC | BIC | BIC | |
| Indep | 1711200 | 1709446 | 1837982 |
| HMM | 1633735 | 1632363 | 1778867 |
| NHMM: Annot | 1632220 | 1630790 | 1775630 |
| NHMM: Assay | 1633350 | 1631917 | 1776883 |
| NHMM: Dist | 1625176 | 1623628 | 1764338 |
| NHMM: CpG | 1632316 | 1630918 | 1774458 |
| NHMM: GC | 1633613 | 1632222 | 1777564 |
| NHMM: Dist+Annot | 1623574 | 1622009 | 1762342 |
| NHMM: Dist+CpG | 1624100 | 1622709 | 1774413 |
| NHMM: Dist+GC | 1625293 | 1623703 | 1764196 |