Single-feature polymorphism discovery in the barley transcriptome

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.

ISSN: 1474-760X