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Table 3 Comparison of MIV and IIV. We compare MIV and IIV input data with respect to the sets of genes ultimately identified as differentially expressed. The genotype and set labelings are the same as those in Table 1. The GP model was used to analyze the unnormalized MIV and IIV data from Experiment 1. The GOT model was used to analyze the unnormalized MIV and IIV data from Experiment 2. Up-expressed and down-expressed counts are reported for both experiments and all genotypes. The count of genes in the intersections is found in column Common. For convenience, percentages of the intersection with respect to the MIV and IIV sets are tabulated in the last two columns. The ALL entries correspond to the H1 hypotheses of the GOT model (see Materials and Methods).

From: The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison

Genotype   MIV IIV Common % of common in MIV % of common in IIV
   GP Model — Experiment 1
WT + 725 567 501 69.10% 88.36%
WT - 774 552 515 66.54% 93.30%
antiPLD + 518 422 357 68.92% 84.60%
antiPLD - 505 336 313 61.98% 93.15%
   GOT Model — Experiment 2
Col-0 + 311 227 198 63.67% 87.22%
Col-0 - 190 122 110 57.89% 90.16%
Cvi-0 + 185 106 89 48.11% 83.96%
Cvi-0 - 97 63 59 60.82% 93.65%
ws + 326 234 181 55.52% 77.35%
ws - 482 331 273 56.64% 82.48%
Th + 363 238 219 60.33% 92.02%
Th - 251 196 166 66.14% 84.69%
ALL + 448 298 249 55.58% 83.56%
ALL - 294 202 159 54.08% 78.71%