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Table 2 Comparison of different methods for the simulated data set with 2,100/2,058 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 = 0.03, q = 0.08)
HGMM
Sample D FDR D FDR D FDR D FDR D FDR D FDR
GSM254930 2159 0.23 1694 0.17 2219 0.28 1475 0.004 1619 0.004 1605 0.03
GSM254971 1965 0.21 2033 0.22 2187 0.30 1395 0.003 1578 0.006 1577 0.03
GSM254972 2015 0.19 2226 0.27 2151 0.27 1553 0.003 1713 0.009 1553 0.03
GSM254973 1575 0.14 1929 0.19 2094 0.28 1334 0.004 1504 0.008 1520 0.02
GSM254805 1982 0.30 1764 0.24 1671 0.27 1034 0.013 1140 0.019 939 0.03
GSM254806 2180 0.27 2344 0.33 1910 0.23 1404 0.008 1687 0.027 1372 0.03
GSM254807 1495 0.14 1926 0.18 2034 0.27 1486 0.003 1655 0.009 1519 0.03
  1. See main text for the simulation methods. Approximately 4.3% of the probes are from spike-in regions.