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364
Affymetrix GeneChip
®
Genotyping Analysis Software User’s Guide
The samples and SNPs in Figure D.4 are part of HapMap, and
therefore allow an independent estimate of the genotype for each case,
indicated by the color of each point (AA = red, AB = blue,
BB = green). In each plot, the prior estimates of cluster centers and
variances are indicated in the light gray x’s and ellipses. Note that
because a generic prior is used for all SNPs, the prior is the same for
both examples. The cluster centers and variances from the observed
data, estimated by using DM with a stringent 0.17 threshold for
seeding, are indicated by the black x’s and ellipses. The posterior
estimates of cluster centers and variances are indicated by the magenta
x’s and ellipses. In all cases, the ellipses extend to a Mahalanobis
distance of 2 from the cluster center. One thing to note is that in both
SNPs, the heterozygote and major homozygote clusters, the posterior
estimate is essentially the same as the estimate provided by the data,
which is the desired result. There is sufficient data available for these
clusters that the prior is overridden. For the minor homozygotes, the
posterior estimate is more strongly influenced by the prior, since there
are few data available for this rare genotype. A second thing to note is
that this clustering approach is comfortably handling the
phenomenon of unequal allele signals for A and B alleles – particularly
Figure D.4
Examples of SNP clustering
GTYPE_manual.book Page 364 Wednesday, August 2, 2006 11:31 AM