Table 6 |
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|
Type 1 error (when effect size is 0) in simulation studies |
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|
Causal gene set |
Gene set size |
Gene size |
Significance level |
Z-statistic method |
SNP-PRAGE |
GLOSSI |
GSEA |
||||||||
|
|
|||||||||||||||
|
m |
m |
||||||||||||||
|
1 |
2 |
3 |
4 |
5 |
1 |
2 |
3 |
4 |
5 |
||||||
|
|
|||||||||||||||
|
Set1 |
20 genes |
9~12 SNPs |
0.05 0.01 |
.005 .002 |
.003 .002 |
.004 .003 |
.004 .002 |
.003 .001 |
.057 .013 |
.053 .009 |
.054 .010 |
.054 .011 |
.053 .010 |
.052 .010 |
.051 .011 |
|
|
|||||||||||||||
|
Set2 |
20 genes |
20~30 SNPs |
0.05 0.01 |
.083 .033 |
.087 .035 |
.084 .034 |
.080 .031 |
.080 .031 |
.051 .011 |
.052 .011 |
.052 .009 |
.050 .008 |
.052 .008 |
.051 .009 |
.049 .010 |
|
|
|||||||||||||||
|
Set3 |
20 genes |
36~49 SNPs |
0.05 0.01 |
.430 .144 |
.641 .294 |
.760 .429 |
.864 .634 |
.891 .671 |
.047 .008 |
.049 .010 |
.050 .010 |
.050 .011 |
.051 .011 |
.049 .011 |
.052 .012 |
|
|
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|
Lee et al. BMC Systems Biology 2011 5(Suppl 2):S11 doi:10.1186/1752-0509-5-S2-S11 |
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