Newport iServer MicroServer iTHX-M Operator's Manual page 336

DETERMINING SAMPLE GENDER
328
Affymetrix GeneChip ®
Calling the Allele
The algorithm compares the sample's call zone scores for the three
possible allele calls to the algorithm's call zone bound, also known as
the call zone radius.
• If the sample's call zone score for a particular allele is lower than
the call zone bound, the SNP is assigned that allele call, and that
call zone score is displayed in the SNP table of the MPAM
mapping analysis window.
• If the sample's call zone score is greater than the call zone bound
for all of the allele calls, the SNP is declared a No Call.
The call zone bound can be adjusted using the CallZoneBound
parameter (see
MPAM Mapping Algorithm Settings, on page 331
If you change the CallZoneBound parameter you may also wish to
change the Call Zone Radius value displayed in the RAS Scatter Plot
or the MPAM mapping analysis window (see
page 164).
Gender-specific models are used for genotyping of SNPs on the X
chromosome because males only have homozygous, AA or BB calls
(Figure B.5), while females can have AA, AB, or BB calls
Genotyping Analysis Software User's Guide
MPAM Scatter Plot, on
(Figure B.6).
).