A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays

Table 3 Number of SFPs detected by transcript cRNA hybridization

Tissue type	Shoot	Young panicle	Intersect^a	Union^b
Total probe sets	12,620	12,538	11,112	15,768
(Total probes)	(121,763)	(120,708)	(107,129)	(171,482)
SFP probes	6,657	6,549	5,573	7,633
Called	4,324	4,467	3,382	5,409
TRUE	3,393	3,513	2,812	4,094
	51.0%	53.6%	50.5%	53.6%
FALSE	931	954	570	1,315
	21.5%	21.4%	16.9%	24.3%
Genome^c	2,150	2,208	1,818	2,540

The probe sets with intensity above log₁₀-2.5 for both Nipponbare and 93-11 genomes were surveyed. Called indicates the number of probes detected as SFP probes at p < 10^-6 by SNEP. TRUE and FALSE are same as in Table 2. ^a, the case applied to the both shoot and young panicle. ^b, the case applied to either shoot or young panicle. ^c, the number of SFPs detected by whole-genome hybridization in TRUE.

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