Table 1.
Benchmark datasets
| ID | GEO ID | Tissue | Disease status | # Samples | # Missing values (21k) | % Missing values (21k) |
|---|---|---|---|---|---|---|
| D1 | GSE32146 | Colon mucosa | Crohn’s disease | 10 | 175 | 0.08% |
| D2 | GSE32146 | Colon mucosa | Ulcerative colitis | 5 | 161 | 0.15% |
| D3 | GSE32146 | Colon | Normal | 10 | 171 | 0.08% |
| D4 | GSE32148 | Blood | Normal | 19 | 325 | 0.08% |
| D5 | GSE40005 | Blood | Normal | 12 | 324 | 0.13% |
| D6 | GSE42921 | Colon mucosa | Crohn’s disease | 5 | 192 | 0.18% |
| D7 | GSE42921 | Colon mucosa | Ulcerative colitis | 6 | 331 | 0.26% |
| D8 | GSE42921 | Colon | Normal | 12 | 874 | 0.34% |
| D9 | GSE43091 | Liver | Cancer | 50 | 1,980 | 0.19% |
| D10 | GSE43091 | Liver | Normal | 4 | 125 | 0.15% |
| D11 | GSE44684 | Cerebellum | Normal | 6 | 67 | 0.05% |
| D12 | GSE49393 | Prefrontal Cortex | Normal | 25 | 54,000 | 10.11% |
| D13 | GSE51388 | Blood | Normal | 60 | 292,200 | 22.79% |
| D14 | GSE52113 | Blood | Normal | 24 | 0 | 0.00% |
| D15 | GSE53051 | Breast | Cancer | 14 | 0 | 0.00% |
| D16 | GSE53051 | Colon | Cancer | 35 | 0 | 0.00% |
| D17 | GSE53051 | Colon, Pancreas | Normal | 9 | 0 | 0.00% |
| D18 | GSE53051 | Lung | Cancer | 9 | 0 | 0.00% |
| D19 | GSE53051 | Pancreas | Cancer | 29 | 0 | 0.00% |
| D20 | GSE53051 | Thyroid | Cancer | 70 | 0 | 0.00% |
| D21 | GSE53162 | Brain, Cerebellum, Prefrontal Cortex | Normal | 21 | 0 | 0.00% |
| D22 | GSE53740 | Blood | Normal | 165 | 0 | 0.00% |
| D23 | GSE57360 | Brain | Normal | 5 | 0 | 0.00% |
| D24 | GSE61151 | Blood | Normal | 184 | 7,544 | 0.19% |
| D25 | GSE61257 | Adipose | Non-alcoholic fatty liver disease (NAFLD) | 8 | 88 | 0.05% |
| D26 | GSE61257 | Adipose | Non-alcoholic steatohepatitis (NASH) | 9 | 142 | 0.07% |
| D27 | GSE61257 | Adipose | Normal | 15 | 241 | 0.08% |
| D28 | GSE61258 | Liver | Non-alcoholic fatty liver disease (NAFLD) | 14 | 370 | 0.12% |
| D29 | GSE61258 | Liver | Non-alcoholic steatohepatitis (NASH) | 7 | 218 | 0.15% |
| D30 | GSE61258 | Liver | Normal | 32 | 966 | 0.14% |
| D31 | GSE61258 | Liver | Primary biliary cholangitis (PBC) | 12 | 251 | 0.10% |
| D32 | GSE61258 | Liver | Primary sclerosing cholangitis (PSC) | 14 | 352 | 0.12% |
| D33 | GSE61259 | Muscle | Non-alcoholic fatty liver disease (NAFLD) | 9 | 90 | 0.05% |
| D34 | GSE61259 | Muscle | Non-alcoholic steatohepatitis (NASH) | 7 | 49 | 0.03% |
| D35 | GSE61259 | Muscle | Normal | 10 | 96 | 0.04% |
| D36 | GSE61380 | Brain | Normal | 15 | 2,4671 | 7.70% |
| D37 | GSE62003 | Blood | Normal | 35 | 0 | 0.00% |
| D38 | GSE64495 | Blood | Normal | 106 | 32 | 0.00% |
| D39 | GSE67477 | Liver | Cancer | 6 | 461 | 0.36% |
| D40 | GSE67484 | Liver, Intestine-Small | Normal | 4 | 45 | 0.05% |
| D41 | GSE69502 | Brain, Spinal Cord | Normal | 20 | 37,781 | 8.84% |
| D42 | GSE71955 | Blood | Normal | 62 | 260,245 | 19.64% |
| D43 | GSE73103 | Blood | Normal | 268 | 1,005,268 | 17.55% |
| D44 | GSE73747 | Brain | Normal | 9 | 7,069 | 3.68% |
| D45 | GSE79122 | Brain | Normal | 7 | 99 | 0.07% |
| D46 | GSE80970 | Prefrontal Cortex | Normal | 68 | 1,324 | 0.09% |
| D47 | GSE82218 | Blood | Normal | 25 | 398 | 0.07% |
| D48 | GSE84003 | Blood | Normal | 6 | 275 | 0.21% |
| D49 | GSE88821 | Colon, Rectum | Cancer | 63 | 36,995 | 2.75% |
| D50 | GSE88821 | Colon, Rectum | Normal | 8 | 4,680 | 2.74% |
| D51 | GSE88821 | Liver | Cancer | 4 | 2,349 | 2.75% |
| D52 | GSE89093 | Blood | Normal | 46 | 65,044 | 6.62% |
| D53 | GSE89472 | Blood | Normal | 5 | 245 | 0.23% |
| D54 | GSE89702 | Cerebellum | Normal | 17 | 49,572 | 13.65% |
| D55 | GSE89703 | Hippocampus | Normal | 13 | 37,557 | 13.52% |
| D56 | GSE89705 | Putamen | Normal | 17 | 49,215 | 13.55% |
| D57 | GSE89706 | Putamen | Normal | 28 | 78,736 | 13.16% |
| D58 | GSE97362 | Blood | Normal | 123 | 2,333 | 0.09% |