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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.