From: A class of models for analyzing GeneChip® gene expression analysis array data
Scenario | Calculation | Annotation |
---|---|---|
1. MAS4.0-equivalent | Z jik = (yji 1k- yji 0k) | Direct difference between PM and MM |
2. MAS5.0-equivalent | Z jik = (yji 1k- ) | is the Idealized Mis-match (IM) |
3. PM only | Z jik = yji 1k | Ignore MM |
4. RMA-equivalent | Z jik = log(yji 1k- ) | is the mean background estimated from PM for the kth chip |
5. Log ratio | Z jik = ln(yji 1k/ yji 0k) | Difference on the logarithmic scale |
6. Log difference | Z jik = ln(yji 1k- ) | Difference on the logarithmic scale |
7. Log PM | Z jik = ln(yji 1k) | PM only on the logarithmic scale |
8. Box-Cox on PM | Z jik = ( - 1) / ω | Box-Cox transformation on PM only |
9. Box-Cox on PM-IM | Z jik = [(yji 1k- )ω- 1] / ω | Box-Cox transformation on PM-IM |