Newport iServer MicroServer iTHX-M Operator's Manual page 348

AA Model
PMA MMA PMB MMB
Figure C.3
Examples of models
340
Affymetrix GeneChip ®
• 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.
BB Model
PMA MMA PMB MMB
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:
Calculate four different quantitative log likelihoods
1.
for each model (null, AA, AB, BB), for each of the ten probe
quartets in the SNP's probe set (see below).
Calculate log likelihood ratios (S-values)
2.
model and probe quartet using the quantitative log likelihoods
(see page 342).
Use one-sided Wilcoxon signed-rank test on the S-values
3.
calculate reliability rank scores for each model; the SNP is assigned
to the model with the lowest rank score (see
Genotyping Analysis Software User's Guide
AB Model
PMA MMA PMB MMB
Null Model
PMA MMA PMB
(l-values), one
for each combination of
to
page 343).
MMB