Table 2 Comparison between MAS4 and MOID.
From: Match-Only Integral Distribution (MOID) Algorithm for high-density oligonucleotide array analysis
MAS4 | MOID | |
|---|---|---|
Mismatch used | Yes | No |
Sensitivity to probe set size | Super-Olympic filtering is turned off when remaining probe number is less than 8. | Confidence intervals gradually increase as probe set size drops. |
Relative error (Spiking tests) | 30% | 28% |
Minimum of probes required (Spiking tests) | 10 | 10 |
No-change test results (True fold change = 1.0) | 80% of fold change values in [0.80, 1.34] | 80% of fold change values in [0.92,1.22] |
Normalization | Constant based on average intensity. Normalize once. | Allow both constant and curve normalization. Iterative scheme. |
Problematic genes (Bright mismatches) | May underestimate expression level | May overestimate expression level |
Expression Level | Average difference (may be negative). No confidence interval evaluations | Expression value (always positive) Lower bound and upper bound (with probe set size taken into account. |
Present Call | A, P, M (discrete, unstable). Rules were derived from 50 μm and 24 μm feature arrays, may need update for 20 μm) | Continuous LogP |