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382
Affymetrix GeneChip
®
Genotyping Analysis Software User’s Guide
Where:
where the Total Number Calls does not include the no call samples,
i.e.
Total Number of Calls = Number of AA Calls + Number of BB Calls
+ Number of AB Calls
The Hardy-Weinberg probability is
where CDF is the Cumulative Distributive Function for the chi-
squared distribution.
MENDELIAN ERROR
If you have entered pedigree information for a set of samples from
different members of a family, you can use the Mendelian Error filter
to eliminate SNPs that do not satisfy Mendel Inheritance rules in the
samples. This allows you to identify incorrectly identified samples and
other problems.
The pedigree checking uses a Lange-Goradia algorithm. The
algorithm is able to determine Mendel errors across multiple siblings
and across multiple generations.
SNPs on the X chromosome for males are tested using haploid
inheritance rules. All other chromosomes including the autosomal and
Female X chromosomes shall use automsomal (diploid) rules.
f
a
Number of AA calls
( )
Total Number calls
-----------------------------------------------
=
f
b
Number of BB calls
( )
Total Number calls
----------------------------------------------
=
f
aa
Number of AA calls + 0.5 * Number of AB calls
( )
Total Number calls
-------------------------------------------------------------------------------------------------------------
=
f
bb
Number of BB calls + 0.5 * Number of AB calls
( )
Total Number calls
------------------------------------------------------------------------------------------------------------
=
f
ab
Number of AB calls
( )
Total Number calls
----------------------------------------------
=
p
HW
CDF x
2
( )
=
GTYPE_manual.book Page 382 Wednesday, August 2, 2006 11:31 AM