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Table 2 A list of selected probe measures

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