Robust Significance Analysis of Microarrays by Minimum β-Divergence Method
Table 2
Performance evaluation of different methods using average values of FDR associated with varying proportions of DE gene.
Percentage of DE gene
ANOVA
KW
SAM
LIMMA
EB
GAGA
BRIDGE
Proposed
Average FDR for small-sample case
2%
0.355
0.205
0.215
0.210
0.260
0.405
0.380
0.215
(0.755)
(0.710)
(0.735)
(0.740)
(0.785)
(0.780)
(0.485)
(0.210)
[0.650]
[0.600]
[0.630]
[0.620]
[0.820]
[0.680]
[0.625]
[0.235]
4%
0.280
0.152
0.165
0.168
0.222
0.347
0.322
0.165
(0.748)
(0.720)
(0.720)
(0.720)
(0.785)
(0.775)
(0.390)
(0.168)
[0.595]
[0.575]
[0.572]
[0.572]
[0.792]
[0.632]
[0.398]
[0.200]
6%
0.287
0.197
0.205
0.198
0.252
0.367
0.342
0.200
(0.738)
(0.725)
(0.725)
(0.728)
(0.798)
(0.782)
(0.372)
(0.207)
[0.578]
[0.575]
[0.575]
[0.573]
[0.787]
[0.653]
[0.390]
[0.227]
8%
0.266
0.181
0.196
0.191
0.231
0.318
0.296
0.196
(0.728)
(0.720)
(0.710)
(0.719)
(0.669)
(0.761)
(0.329)
(0.195)
[0.578]
[0.570]
[0.570]
[0.570]
[0.774]
[0.640]
[0.346]
[0.210]
10%
0.239
0.152
0.165
0.156
0.190
0.303
0.285
0.165
(0.585)
(0.574)
(0.563)
(0.571)
(0.569)
(0.639)
(0.305)
(0.163)
[0.564]
[0.553]
[0.563]
[0.563]
[0.773]
[0.646]
[0.310]
[0.178]
Average FDR for large-sample case
2%
0.075
0.080
0.060
0.060
0.110
0.115
0.110
0.060
(0.500)
(0.105)
(0.470)
(0.495)
(0.570)
(0.580)
(0.145)
(0.065)
[0.405]
[0.095]
[0.410]
[0.400]
[0.485]
[0.480]
[0.125]
[0.070]
4%
0.082
0.087
0.085
0.085
0.115
0.117
0.115
0.085
(0.510)
(0.115)
(0.458)
(0.500)
(0.540)
(0.560)
(0.148)
(0.082)
[0.408]
[0.102]
[0.420]
[0.410]
[0.480]
[0.498]
[0.125]
[0.088]
6%
0.090
0.092
0.088
0.086
0.101
0.111
0.11
0.088
(0.515)
(0.118)
(0.453)
(0.510)
(0.530)
(0.533)
(0.145)
(0.088)
[0.400]
[0.113]
[0.403]
[0.398]
[0.460]
[0.467]
[0.125]
[0.087]
8%
0.070
0.070
0.06
0.072
0.096
0.115
0.109
0.069
(0.460)
(0.104)
(0.384)
(0.450)
(0.459)
(0.459)
(0.134)
(0.069)
[0.398]
[0.081]
[0.416]
[0.398]
[0.465]
[0.471]
[0.120]
[0.075]
10%
0.062
0.063
0.057
0.057
0.075
0.091
0.087
0.059
(0.361)
(0.079)
(0.299)
(0.347)
(0.355)
(0.363)
(0.104)
(0.060)
[0.395]
[0.080]
[0.409]
[0.396]
[0.443]
[0.458]
[0.098]
[0.063]
In this table the values within the brackets (⋅), , and [⋅] represent the average values of FDR estimated by different methods (ANOVA, KW, SAM, LIMMA, EB, GAGA, BRIDGE, and proposed) in presence of one or two outliers in each of 10%, 20%, and 50% genes, respectively.
