Table 1.

False discovery rates for present and marginally present classifications

	5%			10%			17%
	P value	FP	TP	P value	FP	TP	P value	FP	TP
Raw PM and MM	0.008	1,098	19,398	0.025	2,291	20,182	0.060	4,300	20,687
GC-RMA PM and MM	0.024	1,127	20,013	0.111	2,372	20,607	0.216	4,136	20,944
GC-RMA MM threshold	0.037	1,107	19,969	0.111	2,392	20,621	0.235	4,202	21,003

The number of false positives (FPs) and true positives (TPs) is for a given percentage of false positives out of the total number of positives (5%, 10% and 17% but percentages for each method are not exact due to P value granularity) and the corresponding P value cutoff for the MAS 5.0 present/absent calls. The calculations are based on a total of 60,624 true negatives (10,104 empty probesets in 6 replicates) and 23,436 true positives (3,906 probesets that can be aligned to transcripts in six replicates). The default P value cutoff is 0.060 for separating marginally present from absent transcripts.