Table 2 Filtering per array.
From: Limitations of mRNA amplification from small-size cell samples
| Â | 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) |
| Â | 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) |
| Â | 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>2Ă— standard deviation of background | 113 | 261 | 3459 | 2455 | 2229 | 1390 | 1651 (1198) | 1602 | 562 | 2020 | 1292 | 3886 | 2184 | 1924 (1023) |
| Â | 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) |
| Â | 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% |