Table 7. Eliminating the poorest quality samples.

Example of a strategy that used all three sample cut-points and eliminated the poorest quality samples and chips. The criteria applied for inclusion were: AFS = 0 AND pH ≥ 6.6 AND 28S/18S ≥ 1.5. The samples that passed all three measures were placed into the ‘included’ group and the remaining were placed in the group ‘excluded.’ The two groups were compared by t-test separately in two brain regions. The significant p-values are in bold. The abbreviations are the same as Table 1. The microarray chip quality was improved in the included compared to the excluded samples.

		Clinical Quality		Tissue Quality			RNA Quality				Microarray Chip Quality
Brain	Criteria	Age	AFS 0 / ≥1	pH	PMI (hours)	Freezer Time (years)	28S/18S	3′/5′ GAPDH	3′/5′ ACTB	RIN**	%PC	SF	ACI	Type 1/2 1 / 2***
ACC	Include (n = 60)	49.43 (13.76)	N/A	6.93 (0.16)	22.96 (7.79)	3.35 (3.36)	1.98 (0.22)	1.46 (0.37)	2.49 (1.42)	5.94 (0.93)	44.00 (4.23)	1.07 (1.03)	0.97 (0.02)	56 / 4
	Exclude (n = 38)	56.26 (12.05)	N/A	6.66 (0.26)	25.52 (9.19)	2.51 (3.41)	1.51 (0.36)	2.03 (0.93)	3.60 (2.13)	5.67 (1.58)	41.47 (6.25)	1.97 (2.08)	0.92 (0.05)	12 / 24
	p-value	0.01	N/A	N/A	0.16	0.24	N/A	0.00074	0.0006	0.35	0.03	0.02	<0.000005	<0.000005
CB	Include (n = 59)	50.20 (13.81)	N/A	6.94 (0.16)	23.44 (7.99)	3.11 (3.24)	2.06 (0.34)	1.42 (0.48)	3.02 (2.74)	7.11 (1.31)	45.96 (3.08)	1.66 (3.10)	0.98 (0.02)	57 / 2
	Exclude (n = 32)	54.31 (11.75)	N/A	6.62 (0.25)	24.25 (9.26)	3.22 (3.73)	1.57 (0.50)	2.16 (0.97)	4.54 (3.33)	5.72 (1.81)	40.20 (6.86)	4.24 (5.28)	0.92 (0.07)	7 / 25
	p-value	0.14	N/A	N/A	0.68	0.89	N/A	0.0002	0.03	0.002	0.00006	0.02	0.0005	<0.000005

^*N/A. The a priori selection of quality by AFS, pH, and RNA produced highly significant differences in these 3 measures; therefore the p-value was not shown.

^**RIN calculation for ACC only included part of the sample due to technical difficulties in the Agilent run.

^***Type 1 / 2 p-values were calculated by Fisher's exact test.