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Table 4 Effects of low expressed gene elimination on SFP detection performances in transcript hybridization by SNEP.

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

Tissue type Shoot
Expressed
Shoot All Young panicle All Young panicle All
Total probe sets 12,620 41,525 12,538 41,525
Total probes 121,763 391,818 120,708 391,818
SFP probes 6,657 58,150 6,549 58,150
SNEP threshold 10-6.0 10-6.0 10-11.25 10-6 10-6.0 10-10.05
Called 4,324 7,793 5,136 4,467 7,492 5,727
TRUE 3,393 5,442 4,030 3,513 5,440 4,502
  51.0% 9.4% 6.9% 53.6% 9.4% 7.7%
FALSE 931 2,351 1,106 954 2,092 1,225
  21.5% 30.2% 21.5% 21.4% 27.4% 21.4%
  1. Numbers of "Shoot Expressed" and "Young panicle Expressed" were from Table 3. Numbers of SNEP analyses for "all" were summarized both at the same SNEP threshold, 10-6, and at the same FPR of "Expressed".