Table 3.
Evaluation of hybridization signal intensities on PlasTi-microarrays
| Experiment | A | B | C | D | E |
|---|---|---|---|---|---|
| Overall spot intensity characteristics | |||||
| Amean | 9.509 | 10.164 | 10.819 | 10.122 | 10.269 |
| Norm. min (Amin/Amean) | 0.508 | 0.797 | 0.784 | 0.814 | 0.770 |
| Norm. max (Amax/Amean) | 1.535 | 1.462 | 1.362 | 1.444 | 1.401 |
| "Coding" probes with Aprobe > Amean | 287 (91.11%) | 254 (80.63%) | 286 (90.79%) | 268 (85.08%) | 277 (87.94%) |
| "Non-coding" probes with Aprobe > Amean | 267 (20.32%) | 226 (17.20%) | 225 (17.12%) | 203 (15.45%) | 245 (18.65%) |
| Non-specific signal characteristics | |||||
| Anegmean | 5.540 | 8.276 | 8.571 | 8.317 | 7.989 |
| BUFFER (Abuffmean/Anegmean) | 1.021 ± 0.160 | 0.999 ± 0.020 | 1.002 ± 0.027 | 1.002 ± 0.026 | 1.001 ± 0.034 |
| EMPTY (Aemptymean/Anegmean) | 0.916 ± 0.043 | 0.993 ± 0.018 | 0.989 ± 0.013 | 0.990 ± 0.014 | 0.987 ± 0.010 |
| ALIEN (Aalienmean/Anegmean) | 1.031 ± 0.155 | 1.000 ± 0.026 | 1.001 ± 0.027 | 1.001 ± 0.022 | 1.002 ± 0.029 |
| Athr | 7.288 | 8.862 | 9.125 | 8.799 | 8.637 |
| Probes with Aprobe > Athr | 1094 (67.16%) | 1298 (79.68%) | 1244 (76.36%) | 1250 (76.73%) | 1225 (75.20%) |
Amean is the mean intensity of all probes on all microarrays within the experiment. Anegmean is the mean intensity of all negative control spots on all microarrays within the experiment. Norm.min and Norm.max are normalized minimal and maximal intensity values. Athr is a threshold intensity value qualifying the probe as "detected" and was calculated from the formula Athr = Anegmean + 2 SD. Experiments A-E are briefly described in the Additional file 3.