Table 1

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

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.

Rostoks et al. Genome Biology 2005 6:R54   doi:10.1186/gb-2005-6-6-r54

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