Table 1. Results of an experimental approach to find the best threshold of magnitude (|ALR|) and probability (P) of differentially expressed transcripts between MK801-treated and control animals.

|ALR|	P	EXP	Boot 1	Boot 2	Boot 3	FDR (%)
0.585	0.05	74	39	12	14	34.5
0.848	0.05	24	15	5	3	41.7
0.585	0.01	15	11	4	2	50.0
0.848	0.01	3	3	1	0	66.7
0.263	0.005	46	25	12	5	40.2
0.585	0.005	4	3	1	2	50.0
0.848	0.005	1	0	0	0	0.0

Abbreviations: |ALR|, absolute average log2 ratio; Boot 1–3, number of probes surpassing the same criteria in permutation comparisons; EXP, number of probes meeting the |ALR| and P criteria for difference in expression between MK801- and control animals; FDR, false discovery rate.