Newport iServer MicroServer iTHX-M Operator's Manual page 332

CALCULATING MEDIAN RELATIVE ALLELE SIGNALS (RAS)
324
Affymetrix GeneChip ®
The relative allele signal is a measure of the intensities of the perfect
match cells for the A and B alleles of a SNP. The algorithm calculates
median relative allele signal scores (RAS) for the sense and antisense
strands of the SNP, using the intensity values for the probe cells:
The RAS value for each probe quartet is calculated using the
1.
following steps:
The MisMatch Average, M, for the quartet is calculated.
A.
M = [M + M
A B
Where:
M = Mismatch A allele intensity value
A
M = Mismatch B allele intensity value
B
The MPAM mapping algorithm calculates the relative
B.
intensity values for the A and B alleles.
A =Max [P
A
B =Max [P
B
Where:
= Perfect Match A allele intensity value
P A
= Perfect Match B allele intensity value
P B
The MPAM mapping algorithm uses these values to calculate
C.
the RAS value for the probe quartet:
RASquartet =A/ A + B
The algorithm calculates the median of the RAS values for the
2.
sense direction probe quartets and uses this value as the Median
RAS value for the sense direction. The algorithm calculates the
Genotyping Analysis Software User's Guide
] / 2
M, 0]
M, 0]