TABLE 3.

Comparison of positive probes identified by probe design criteria, by the Student t test, and by SNR thresholds^a

Identifier	Threshold	No. of identified positives (% of t test positives)b
		PRc > 50%	PR > 70%	PR > 90%
SSR	2.0	58 + 7 + 21 = 86 (113)	58 + 5 + 19 = 82 (108)	57 + 3 + 18 = 78 (103)
SBR	1.6	58 + 8 + 25 = 91 (120)	57 + 6 + 23 = 86 (113)	56 + 4 + 20 = 80 (105)
SSDR	0.70	59 + 4 + 18 = 81 (107)	59 + 3 + 17 = 79 (104)	58 + 1 + 16 = 75 (99)

^aSNR threshold-identified positive probes at different positive rates; 368 probes were valid for analysis when 500 ng of labeled S. oneidensis MR1 gDNA hybridized with the array. Five slides were used with four replicates in each slide, so each probe had up to 20 spots.

^bThe first three numbers are the size of the defined positive probe pool, the size of the defined negative probe pool, and the number of ignored probes based on defined positive, negative, and ignored probe pools.

^cPR = (number of positive spots identified by SNR thresholds × 100)/total number of spots for each probe.