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340
Affymetrix GeneChip
®
Genotyping Analysis Software User’s Guide
• Null: Intensities for both PM and MM are all background
intensities.
• AA: The PM cell intensity for the A allele is high and the other
three cells are background.
• AB: The PM cell intensities for the A and B alleles are high and
the MM cell intensities are background.
• BB: The PM cell intensity for the B allele is high and the other
three cells are background.
For each model, Dynamic Model assumes that the background
intensities are the same and smaller than the foreground intensities.
The Dynamic Model mapping algorithm uses the following steps:
1.
Calculate four different quantitative log likelihoods (l-values) , one
for each model (null, AA, AB, BB), for each of the ten probe
quartets in the SNP’s probe set (see below).
2.
Calculate log likelihood ratios (S-values) for each combination of
model and probe quartet using the quantitative log likelihoods
(see
page 342) .
3.
Use one-sided Wilcoxon signed-rank test on the S-values to
calculate reliability rank scores for each model; the SNP is assigned
to the model with the lowest rank score (see
page 343) .
Figure C.3
Examples of models
AA Model
PMA MMA PMB MMB
BB Model AB Model Null Model
PMA MMA PMB MMB PMA MMA PMB MMB PMA MMA PMB MMB
GTYPE_manual.book Page 340 Wednesday, August 2, 2006 11:31 AM