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Table 2 Observed FDR for each cut-off value for the three SPP prediction methods

From: Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.)

a. MSA Observed Permuted
  Delta 0.2 14.50% 36.45%
  Delta 0.4 13.80% 17.54%
  Delta 0.6 11.00% 10.85%
  Delta 0.8 10.20% 8.34%
  Delta 1.0 9.80% 7.27%
  Delta 1.2 9.10% 6.80%
  Delta 1.4 8.50% 6.58%
  Delta 1.6 7.90% 6.45%
b. SFPdev Observed Permuted
  FDR 0.10 24.30% 10.00%
  FDR 0.05 21.40% 5.00%
  FDR 0.01 20.10% 1.00%
c. DP Analysis Observed Permuted
  SFPDev 1.2 2.80% N/A
  SFPDev 1.5 1.70% N/A
  SFPDev 2.0 1.10% N/A
  1. Table 2 shows the observed and permuted FDRs for each of the three SPP detection methods. a) Delta values from 0.2 to 1.6 for MSA analysis show decreasing FDRs as stringency increases. At values lower than 0.6 the observed values surpass those expected by permutation analysis. b) Three cutoff values for SFPdev were reported from 10% to 1%. Observed values did not change drastically as permuted stringencies increased. c) Observed FDR values in DP analysis were low and did not drastically change as cutoff values increased.