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Table 1 Comparison of different methods for the original data set

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

  Mixer
(Lowess)
Mixer
(MA2C)
MA2C TileMap
(p = 0.01, q = 0.05)
TileMap
(p = 0.002, q = 0.02)
HGMM
Sample D FDR D FDR D FDR D FDR D FDR D FDR
GSM254930 108 0.28 503 0.84 241 0.66 85 0.08 84 0.07 111 0.20
GSM254971 100 0.28 113 0.37 227 0.64 86 0.09 85 0.09 N/A N/A
GSM254972 98 0.29 195 0.61 178 0.53 84 0.07 88 0.08 N/A N/A
GSM254973 98 0.24 92 0.23 146 0.45 71 0.07 73 0.07 N/A N/A
GSM254805 66 0.20 153 0.56 116 0.43 81 0.22 52 0.09 N/A N/A
GSM254806 89 0.19 184 0.61 85 0.19 236 0.66 143 0.42 89 0.18
GSM254807 97 0.24 102 0.26 100 0.21 76 0.08 91 0.13 123 0.32
  1. The first four samples, GSM254930, GSM254971, GSM254972, and GSM254973 were spiked with unamplified DNA, while the last three samples GSM254805, GSM254806, and GSM254807 were spiked with amplified DNA. Among the total of 385,149 probes, about 820 (~0.2%) of them are from spike-in regions. We did not obtain results of HGMM for some arrays (N/A) due to failure of function HGMM.