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Table 1 Number of DEGs Identified for Case Studies

From: Filtering for increased power for microarray data analysis

    Filtering Method
Case Study Preprocessing Method FDR Method None Detection Call Variance (log2) Variance (original) Signal
Wheat Comp 1 RMA None 15511 12524 12601 12932 12459
   BH 8546 9355 9464 9725 9163
   q-value 10333 12237 12369 13125 12233
Wheat Comp 1 MAS5 None 12547 10520 3497 10728 10539
   BH 5869 6896 1096 7088 6880
   q-value 6687 8968 1137 9305 8989
Wheat Comp 1 PLIER None 17224 13127 8151 13992 13305
   BH 9713 9811 5436 10714 9913
   q-value 12167 13366 6010 15541 14242
Wheat Comp 2 RMA None 10309 7454 7751 7776 7391
   BH 643 1593 1733 1704 1329
   q-value 1416 3390 3874 3791 3175
Wheat Comp 2 MAS5 None 8149 6187 2620 6353 6201
   BH 162 569 42 585 511
   q-value 328 1337 53 1485 1330
Wheat Comp 2 PLIER None 10928 7473 5690 8150 7539
   BH 1048 1654 1219 2109 1633
   q-value 2067 3386 1736 4402 3366
Diabetes RMA None 3469 3043 2710 3018 2991
   BH 644 781 710 807 783
   q-value 728 892 778 904 884
Diabetes MAS5 None 3097 2599 1555 2597 2595
   BH 412 481 239 484 478
   q-value 449 520 241 523 517
Diabetes PLIER None 3266 2895 1792 2912 2921
   BH 541 646 388 682 665
   q-value 615 765 440 793 759
Smoking RMA None 3414 2511 2155 2196 2146
   BH 126 155 143 135 107
   q-value 135 184 177 158 121
Smoking MAS5 None 3684 2522 1843 2510 2506
   BH 112 145 109 146 137
   q-value 130 166 116 164 155
Smoking PLIER None 3097 1832 1824 1704 1643
   BH 64 80 78 77 70
   q-value 70 91 85 81 72
  1. Table of number of probe sets identified as differentially expressed for each of the case studies. For each case study, we considered three preprocessing methods (RMA, MAS5 and PLIER), two FDR methods (Benjamini-Hochberg and q-value) and three filtering methods (MAS detection call, variance (on both the log2 and original scales) and signal). The stated significance level was 0.05 for all methods.