Table 5. Adaptive determination of threshold for spot intensity relative to background intensity.
| |
Number of spots applicable |
% remaining |
Threshold |
|
|---|---|---|---|---|
| ch1 | ch2 | |||
| Mopo | 684 331 | 19.9 | 15.62 (13.60) | 10.53 (12.98) |
| Mopo-clin | 171 285 | 14.5 | 3.98 (3.07) | 4.13 (3.52) |
| Lymphoma | 1 119 833 | 70.2 | 1.83 (1.36) | 1.30 (0.15) |
| DNR | 29 836 | 66.4 | 113 (35.4) | 335 (117.8) |
The ‘Number of spots applicable’ column shows the total number of spots applicable to filtering in each data set. The ‘% remaining’ column shows the percentage of applicable spots that met the array specific quality-filtering criteria. For the DNR data set we found the spot minus background difference to be more useful than the SB ratio as a ‘quality-index’ to use for filtering. For the other data sets, data shown are for filtering based on the SB ratio. The ‘Threshold’ columns show the averages and the standard errors, in parentheses, of the array-specific filtering thresholds found for each data set and each channel.