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Table 2 Observed type I error rates for low nominal error rates

From: Linear models enable powerful differential activity analysis in massively parallel reporter assays

Nominal edgeR DESeq2 QuASAR mpralm mpralm FET t-test
error rate     (agg) (avg)   
Tewhey - large      
1.62e-05 8.21e-04 8.22e-04 1.97e-03 1.64e-04 NA 2.82e-01 0
  (5/6088) (5/6084) (12/6088) (1/6088)   (1718/6088) (0/6088)
1.03e-05 6.57e-04 8.22e-04 1.64e-03 0 NA 2.73e-01 0
  (4/6088) (5/6084) (10/6088) (0/6088)   (1663/6088) (0/6088)
7.25e-06 4.93e-04 8.22e-04 1.64e-03 0 NA 2.66e-01 0
  (3/6088) (5/6084) (10/6088) (0/6088)   (1618/6088) (0/6088)
6.25e-06 4.93e-04 6.57e-04 1.64e-03 0 NA 2.62e-01 0
  (3/6088) (4/6084) (10/6088) (0/6088)   (1597/6088) (0/6088)
Tewhey - targeted      
1.62e-05 5.71e-04 5.71e-04 1.71e-03 5.71e-04 NA 2.57e-02 0
  (2/3503) (2/3503) (6/3503) (2/3501)   (90/3503) (0/3503)
1.03e-05 5.71e-04 5.71e-04 1.71e-03 5.71e-04 NA 2.37e-02 0
  (2/3503) (2/3503) (6/3503) (2/3501)   (83/3503) (0/3503)
7.25e-06 5.71e-04 5.71e-04 1.43e-03 5.71e-04 NA 2.14e-02 0
  (2/3503) (2/3503) (5/3503) (2/3501)   (75/3503) (0/3503)
6.25e-06 5.71e-04 5.71e-04 1.43e-03 5.71e-04 NA 2.00e-02 0
  (2/3503) (2/3503) (5/3503) (2/3501)   (70/3503) (0/3503)
Inoue      
1.62e-05 1.64e-03 2.05e-03 4.1e-04 0 4.1e-04 3.69e-03 4.1e-04
  (4/2440) (5/2440) (1/2440) (0/2440) (1/2440) (9/2440) (1/2440)
1.03e-05 1.64e-03 2.05e-03 4.1e-04 0 4.1e-04 3.28e-03 4.1e-04
  (4/2440) (5/2440) (1/2440) (0/2440) (1/2440) (8/2440) (1/2440)
7.25e-06 8.20e-04 2.05e-03 4.1e-04 0 4.1e-04 2.87e-03 4.1e-04
  (2/2440) (5/2440) (1/2440) (0/2440) (1/2440) (7/2440) (1/2440)
6.25e-06 8.20e-04 2.05e-03 4.1e-04 0 4.1e-04 2.46e-03 4.1e-04
  (2/2440) (5/2440) (1/2440) (0/2440) (1/2440) (6/2440) (1/2440)
Ulirsch      
1.62e-05 0 0 1.09e-03 0 0 4.14e-01 0
  (0/2756) (0/2756) (3/2756) (0/2756) (0/2756) (1140/2756) (0/2756)
1.03e-05 0 0 7.26e-04 0 0 4.06e-01 0
  (0/2756) (0/2756) (2/2756) (0/2756) (0/2756) (1119/2756) (0/2756)
7.25e-06 0 0 7.26e-04 0 0 3.96e-01 0
  (0/2756) (0/2756) (2/2756) (0/2756) (0/2756) (1092/2756) (0/2756)
6.25e-06 0 0 7.26e-04 0 0 3.93e-01 0
  (0/2756) (0/2756) (2/2756) (0/2756) (0/2756) (1083/2756) (0/2756)
Shen      
1.62e-05 2.45e-03 1.67e-02 2.98e-04 0 3e-04 7.39e-01 0
  (8/3264) (51/3052) (1/3358) (0/3286) (1/3337) (2412/3264) (0/3264)
1.03e-05 2.45e-03 1.54e-02 0 0 3e-04 7.33e-01 0
  (8/3264) (47/3052) (0/3358) (0/3286) (1/3337) (2393/3264) (0/3264)
7.25e-06 2.14e-03 1.31e-02 0 0 3e-04 7.30e-01 0
  (7/3264) (40/3052) (0/3358) (0/3286) (1/3337) (2384/3264) (0/3264)
6.25e-06 1.84e-03 1.21e-02 0 0e+00 0e+00 7.29e-01 0
  (6/3264) (37/3052) (0/3358) (0/3286) (0/3337) (2379/3264) (0/3264)