Table 2. Filtering statistics as given with common filtering rules.
| Total number of spots | % flags | % spot < background | % spot <1.4 × background | % spot <100 + background | |
|---|---|---|---|---|---|
| Mopo | 774 144 | 8.00 | 3.12 (2.53) | 18.02 (15.26) | 10.43 (8.84) |
| Mopo-clin | 267 264 | 10.91 | 15.95 (12.10) | 58.62 (48.80) | 50.74 (41.67) |
| Lymphoma | 1 234 944 | 1.20 | 2.45 (2.28) | 33.42 (32.81) | 47.66 (47.06) |
| NCI60 | 630 000 | 0.25 | 5.68 (5.66) | 43.41 (43.28) | 17.92 (17.88) |
| Prostate | 162 500 | NA | NA | NA | NA |
| DNR | 46 208 | 31.91 | 3.41 (0.72) | 7.15 (0.06) | 45.36 (16.25) |
The column ‘Total number of spots’ shows the total number of spots summed over all arrays from each data set. The ‘% flags’ column shows the percentage of spots that had been flagged, manually or by image analysis software, for each data set. The remaining columns show the total percentage of spots that would be removed according to common filtering criteria. For each of these columns, the main number shows the percentage when flagged spots are disregarded in the total number of spots, while the corresponding numbers in parentheses show the percentage of the number of spots also including the spots that were flagged. NA, data not available. The very high number of flagged spots in the DNR data set was due to a flagging procedure included in the GenePix image analysis software.