Table 2.

Filtering per array.

	Arrays hybridized with amplified material								Arrays hybridized with non-amplified material
Array number	1	2	5	6	7	9	10	11	3	4	8	12
Genes flagged by Genepix	5192	2155	1007	2152	3151	2209	3212	1073	4750	4909	2903	4374
	41.55%	17025%	8.06%	17.22%	25.21%	17.68%	25.70%	8.59%	38.01%	39.28%	23.23%	35.00%
Genes flagged manually	15	1	3	5	2	6	10	1	116	15	4223	16
	0.12%	0.008%	0.024%	0.04%	0.016%	0.048%	0.08%	0.008%	0.93%	0.12%	33.79%	0.13%
Additionally Filtered by (spot-background) / background > 1	2078	1621	1055	2081	2081	2033	1680	2596	3226	2223	2117	2521
	16.63%	12.97%	8.44%	16.65%	16.15%	16.27%	13.44%	20.77%	25.81%	17.79%	16.94%	20.17%
Sum	7285	3777	2065	4238	5171	4238	4902	3670	8092	7147	9243	6911
	58.30%	30.22%	16.52%	33.91%	41.38%	33.40%	39.22%	29.37%	64.75%	57.19%	73.96%	55.30%