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Table 3 Comparison of SNP selection using sires with extreme phenotypes vs. using all sires, in terms of predicted residual sum of squares of the best SNP subsets

From: Comparison of classification methods for detecting associations between SNPs and chick mortality

 

Extreme sires

All sires

Stratuma

PRESSb

p-valuec

αd

#SNPsf

PRESSb

p-valuec

K e

#SNPsf

EL

0.638

0.001

0.35

34

0.672

0.001

2

36

EH

0.313

0.001

0.35

35

0.377

0.002

2

33

LL

0.454

0.001

0.35

29

0.519

0.001

2

46

LH

0.510

0.007

0.20

28

0.470

0.001

3

45

  1. a EL = early age-low hygiene; EH = early age-high hygiene; LL = late age-low hygiene; LH = late age-high hygiene.
  2. b predicted residual sum of squares.
  3. c p-value of PRESS, obtained from permutation distribution.
  4. d With extreme sires, two thresholds are determined by α.
  5. e With all sires, K is the number of categories.
  6. f Number of SNPs in the subset.
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Genetics Selection Evolution

ISSN: 1297-9686