Skip to main content

Table 3 Comparison of different methods for the simulated data set with 5,100/4,998 spike-in regions for unamplified/amplified samples, respectively

From: Improved ChIP-chip analysis by a mixture model approach

  Mixer
(Lowess)
Mixer
(MA2C)
MA2C TileMap
(p = 0.01, q = 0.05)
TileMap
(p = 0.08, q = 0.13)
HGMM
Sample D FDR D FDR D FDR D FDR D FDR D FDR
GSM254930 4359 0.16 5753 0.28 4829 0.19 2775 0.001 3872 0.003 3707 0.02
GSM254971 4969 0.23 5110 0.23 4697 0.22 2758 0.001 3682 0.005 3615 0.02
GSM254972 5135 0.22 3957 0.19 4738 0.19 2978 0.001 4114 0.011 3558 0.03
GSM254973 4714 0.18 4795 0.20 4560 0.20 2695 0.001 3534 0.003 3493 0.02
GSM254805 4537 0.25 4784 0.27 3860 0.22 1946 0.003 2744 0.022 2237 0.03
GSM254806 4878 0.21 5826 0.32 4284 0.17 2672 0.0004 3924 0.022 3085 0.03
GSM254807 4957 0.21 5157 0.24 4569 0.20 2487 0.0004 3802 0.003 3508 0.02
  1. See main text for the simulation methods. About 10.2% of the probes are from spike-in regions.