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Table 1 Comparison of the power of the 4 noncollapsing and 2 standard methods

From: Application of noncollapsing methods to the gene-based association test: a comparison study using Genetic Analysis Workshop 18 data

Chromosome Gene Power of methods
   Naïve method Fisher's method Simes' method GSEA method SKAT FamSKAT
3 ABTB1 0.015 0.18 0.025 0 0.075 0.01
3 ARHGEF3 0 0 0 0.035 0.005 0.005
3 B4GALT4 0.015 0 0.015 0.035 0.01 0.015
3 BTD 0 0 0 0.015 0 0
3 CXCR6 0 0 0 0.085 0 0
3 DNASE1L3 0.005 0.005 0.005 0.005 0.04 0.01
3 FBLN2 0.005 0 0 0.035 0 0
3 FLNB 0.01 0.015 0 0.03 0 0
3 LOC152217 0.09 0.145 0.135 0 0.275 0.04
3 MAP4 1 1 1 1 1 1
3 NMNAT3 0.005 0.04 0.005 0 0 0
3 PAK2 0.07 0 0.05 0 0 0
3 PDCD6IP 0.005 0 0.005 0.005 0.04 0.03
3 PPP2R3A 0.045 0.01 0.02 0 0.005 0.005
3 PTPLB 0 0 0 0.02 0.005 0
3 SCAP 0.025 0.005 0.04 0 0.045 0.065
3 SEMA3F 0 0 0 0 0 0
3 SENP5 0 0.02 0.01 0.045 0.01 0.005
3 SUMF1 0.085 0.005 0.06 0.01 0.015 0.005
3 TFDP2 0 0 0 0.035 0 0
3 TUSC2 0.005 0 0.055 0 0.02 0
3 ZBTB38 0.01 0.005 0.01 0.02 0.04 0
  1. Power is calculated based on the analysis of the 200 simulated phenotypic replicates. The largest power for each gene is highlighted in bold.