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Table 3 Evaluation of hybridization signal intensities on PlasTi-microarrays

From: A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants

Experiment A B C D E
Overall spot intensity characteristics
A mean 9.509 10.164 10.819 10.122 10.269
Norm. min (A min /A mean ) 0.508 0.797 0.784 0.814 0.770
Norm. max (A max /A mean ) 1.535 1.462 1.362 1.444 1.401
"Coding" probes with A probe > A mean 287 (91.11%) 254 (80.63%) 286 (90.79%) 268 (85.08%) 277 (87.94%)
"Non-coding" probes with A probe > A mean 267 (20.32%) 226 (17.20%) 225 (17.12%) 203 (15.45%) 245 (18.65%)
Non-specific signal characteristics
Aneg mean 5.540 8.276 8.571 8.317 7.989
BUFFER (Abuff mean /Aneg mean ) 1.021 ± 0.160 0.999 ± 0.020 1.002 ± 0.027 1.002 ± 0.026 1.001 ± 0.034
EMPTY (Aempty mean /Aneg mean ) 0.916 ± 0.043 0.993 ± 0.018 0.989 ± 0.013 0.990 ± 0.014 0.987 ± 0.010
ALIEN (Aalien mean /Aneg mean ) 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 A probe > Athr 1094 (67.16%) 1298 (79.68%) 1244 (76.36%) 1250 (76.73%) 1225 (75.20%)
  1. 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.