Skip to main content

Advertisement

Table 1 SFP false discovery rate (FDR) estimates in RNA and genomic DNA hybridization data

From: Single-feature polymorphism discovery in the barley transcriptome

RNA hybridization: 17 Golden Promise 19 Morex, 6 tissues; SAM analysis for the two-class unpaired case assuming unequal variances; s0 = 0.0342 (the 5% quantile of the s values); number of permutations, 500. Mean number of falsely called genes is computed. Delta p0 Called False FDR
  0.5 0.95 27,159 5,884 0.206
  1.0 0.95 17,744 594 0.032
  1.5 0.95 13,285 65 0.005
  2.0 0.95 10,504 7 0.001
  2.5 0.95 8,583 0 0.000
Genomic DNA hybridization three replicates three genotypes; SAM analysis for the multi-class case with three classes; s0 = 0.0123 (the 25 % quantile of the s values); number of permutations: 100; mean number of falsely called genes is computed. Delta p0 Called False FDR
  1 0.95 4,017 2,073 0.47
  2 0.95 1,728 583 0.31
  3 0.95 1,090 258 0.22
  4 0.95 789 139 0.16
  5 0.95 631 86 0.13
  1. The Bioconductor package siggenes [37,36] was used to derive SFP calls at various thresholds in the original data and randomly permuted data according to SAM [39]. Delta, the threshold; p0, the prior probability of the proportion of SFP in the null dataset; Called, the number of SFP at each threshold; False, the number of SFP in the mean permuted dataset.