Table 2.

Data consistency for the dataset of 537 genes (after data filtering). The pair-wise log ratio correlation squared (LRr², lower triangle) and the percentage of overlapping genes (POG, upper triangle) are listed. T1, T2, and T3 are technical replicates; B1, B2, and B3 are biological replicates. The last three rows/columns (Affymetrix (Aff), Amersham (Ame), and Agilent (Agi)) represent results from the average of the three biological replicates. Gene selection was based on fold-change ranking, and a total of 100 genes (50 genes from each regulation direction) were selected for each comparison. Black bold numbers represent intra-platform technical or biological consistency, or cross-platform concordance.

	Aff.T1	Aff.T2	Aff.T3	Ame.T1	Ame.T2	Ame.T3	Agi.T1	Agi.T2	Agi.T3	Aff.B1	Aff.B2	Aff.B3	Ame.B1	Ame.B2	Ame.B3	Agi.B1	Agi.B2	Agi.B3	Aff	Ame	Agi
Aff.T1	Aff.T1	53	56	52	49	52	50	53	54	71	46	41	53	42	46	52	45	44	58	52	52
Aff.T2	0.5745	Aff.T2	44	51	53	51	48	47	46	70	46	45	53	41	41	47	43	43	61	48	47
Aff.T3	0.5902	0.4525	Aff.T3	52	51	52	53	54	53	69	37	37	53	36	39	53	38	37	48	46	47
Ame.T1	0.5341	0.53	0.572	Ame.T1	88	90	58	60	54	60	39	38	95	55	52	60	37	38	53	76	50
Ame.T2	0.5439	0.537	0.5836	0.9347	Ame.T2	89	56	58	52	59	40	39	92	57	51	58	36	36	55	77	48
Ame.T3	0.5486	0.5499	0.5768	0.9374	0.9482	Ame.T3	57	59	53	59	40	40	94	55	54	58	36	37	55	78	48
Agi.T1	0.4382	0.446	0.5163	0.564	0.5705	0.572	Agi.T1	89	78	57	33	40	59	35	37	89	44	50	50	49	69
Agi.T2	0.4676	0.4847	0.5405	0.5954	0.6009	0.6052	0.9613	Agi.T2	84	57	38	42	62	39	39	93	49	55	53	50	75
Agi.T3	0.4553	0.4617	0.5177	0.5687	0.5729	0.5796	0.9041	0.9419	Agi.T3	56	38	40	55	36	38	88	47	52	50	46	74
Aff.B1	0.858	0.8009	0.8076	0.664	0.6755	0.68	0.5682	0.6059	0.5822	Aff.B1	41	44	60	44	47	57	45	47	64	55	55
Aff.B2	0.4191	0.4626	0.361	0.3498	0.3524	0.3606	0.3054	0.334	0.3301	0.5029	Aff.B2	41	41	47	53	36	54	52	58	46	47
Aff.B3	0.3238	0.417	0.2726	0.3576	0.3766	0.3844	0.3515	0.3834	0.3774	0.4083	0.4451	Aff.B3	40	38	43	41	44	47	74	46	48
Ame.B1	0.5534	0.5502	0.5894	0.9767	0.9807	0.9818	0.5806	0.6129	0.5856	0.6871	0.3616	0.3806	Ame.B1	56	53	61	37	38	55	78	50
Ame.B2	0.4268	0.3686	0.3707	0.6163	0.6253	0.6093	0.313	0.3422	0.3289	0.4719	0.4917	0.2973	0.6297	Ame.B2	71	37	48	46	48	72	43
Ame.B3	0.4137	0.371	0.3575	0.579	0.5647	0.6168	0.3084	0.3389	0.3244	0.4624	0.5056	0.3427	0.5989	0.7859	Ame.B3	37	55	53	52	70	50
Agi.B1	0.4634	0.4739	0.5363	0.5885	0.594	0.5982	0.977	0.9889	0.9686	0.5979	0.3298	0.3784	0.6059	0.3348	0.3306	Agi.B1	47	52	51	50	74
Agi.B2	0.3926	0.3393	0.3296	0.3591	0.3581	0.3627	0.4694	0.5186	0.5031	0.4293	0.5678	0.3239	0.3674	0.5783	0.5682	0.5072	Agi.B2	85	53	45	72
Agi.B3	0.3888	0.3461	0.332	0.355	0.359	0.3598	0.4975	0.541	0.5335	0.4318	0.5659	0.353	0.3654	0.5435	0.5677	0.5349	0.9525	Agi.B3	53	46	78
Aff	0.6397	0.694	0.5684	0.5686	0.5842	0.5934	0.5141	0.5563	0.5432	0.7705	0.7688	0.7978	0.5942	0.5167	0.5437	0.5491	0.5396	0.5566	Aff	58	58
Ame	0.5379	0.4995	0.5108	0.842	0.8412	0.856	0.4661	0.5019	0.4805	0.6277	0.5041	0.3921	0.8639	0.8909	0.8765	0.4931	0.5547	0.5425	0.6341	Ame	51
Agi	0.4877	0.4581	0.4759	0.5176	0.5212	0.5249	0.7747	0.816	0.7989	0.5766	0.5354	0.4123	0.532	0.5341	0.5366	0.8137	0.8863	0.9037	0.6372	0.6098	Agi