Table 2.

Filtering per array.

	Arrays hybridized with sample size 1000 cells							Arrays hybridized with sample size 250 cells
Array number	2	12	1	3	4	11	mean (SD)	6	9	7	5	8	10	mean (SD)
Genes flagged by Genepix	1189	1188	2344	1105	1272	456	1259 (556.2)	1731	1726	1155	1009	4466	3798	2314 (1327)
	10.08%	10.08%	19.98%	9.37%	10.79%	3.87%	10.7%	14.68%	14.64%	9.80%	8.56%	37.88%	32.21%	19.6%
Genes flagged manually	10	17	42	27	21	51	28 (14.3)	21	11	104	359	29	69	98.8 (120.6)
	0.08%	0.14%	0.36%	0.23%	0.18%	0.43%	0.2%	0.18%	0.09%	0.88%	3.04%	0.25%	0.59%	0.8%
Additionally filtered by spot-background>2× standard deviation of background	113	261	3459	2455	2229	1390	1651 (1198)	1602	562	2020	1292	3886	2184	1924 (1023)
	0.01%	2.21%	29.34%	20.82%	18.90%	11.79%	13.9%	13.59%	4.77%	17.13%	10.96%	32.96%	18.52%	16.3%
Sum	1312	1466	5934	3587	3522	1897	2953 (1614)	3354	2299	3279	2660	8381	6051	4337 (2173)
	10.17%	12.43%	49.68%	30.42%	29.87%	16.09%	24.8%	28.45%	19.50%	27.81%	22.56%	71.09%	51.32%	36.8%