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Table 2 Retention counts and percentages. Retention counts (RC) and retention percentages (RP) for the differentially expressed gene sets of Table 1. RC is the number of genes in a set before the MIDAS step that remain in the set after that step. RC is the number of genes in the set before the MIDAS step that remain in the set after that step. RP is the percentage of remaining genes with respect to the number of genes in the set after the MIDAS step. RC and RP are reported for the intersections IIV IIVT, IIVT ∩ IIVTL, IIVTL ∩ IIVTLS, and IIVTLS ∩ IIVTLSF, as well as intersection IIV ∩IIVTLSF, which corresponds to the effect of MIDAS steps from the start of the pipeline to the end. 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

   IIV ∩ IIVT IIVTL IIVTLS IIV ∩
   IIVT IIVTL IIVTLS IIVTLSF IIVTLSF
Genotype   RC RP RC RP RC RP RC RP RC RP
   GP Model — Experiment 1
WT + 545 95.45 74 15.20 285 57.58 456 99.13 59 12.83
WT - 532 96.20 55 11.02 306 61.32 459 99.78 53 11.52
antiPLD + 403 95.72 58 13.18 278 59.02 430 99.77 46 10.67
antiPLD - 326 94.22 45 11.81 203 55.92 330 98.80 33 9.88
   GOT Model — Experiment 2
Col-0 + 224 72.49 221 91.32 219 91.25 172 63.70 159 58.89
Col-0 - 121 70.76 150 84.27 165 91.67 120 65.57 92 50.27
Cvi-0 + 81 75.00 65 79.27 71 91.25 49 69.01 36 50.70
Cvi-0 - 60 64.52 60 81.08 63 88.73 41 61.19 38 56.72
ws + 223 64.45 230 82.44 248 92.19 108 72.00 101 67.33
ws - 293 84.44 267 78.53 314 92.35 180 80.36 149 66.52
Th + 236 59.30 308 88.00 330 90.91 256 70.91 201 55.68
Th - 183 74.69 210 87.14 225 91.46 172 71.67 144 60.00
ALL + 282 65.89 307 85.99 333 94.07 200 68.97 177 61.03
ALL - 196 75.10 196 77.47 230 92.74 133 68.21 103 52.82