As with the gene analysis, the results of the CD analysis (Table 3 and Fig 2) can again serve as a gauge of the relative power of the different gene-set analysis methods. For the self-contained gene-set analysis this comparison is straightforward with MAGMA showing considerably more power than the two PLINK analyses. For the most part MAGMA’s power advantage can be explained by the difference in the underlying gene model, given the superior power of the PC regression model over the SNP-wise model used by PLINK shown before. Differences in how the genes are combined may also play a role however since, in contrast to PLINK, MAGMA weighs genes equally rather than by the number of SNPs in them and explicitly takes correlations between genes into account. Of note is also that PLINK-prune does considerably better than PLINK-avg, and that its p-values are somewhat more strongly correlated with those of the MAGMA analysis (Fig 2). An additional summary statistics analysis (MAGMA-pval-1K) on SNP p-values and using 1,000 Genomes reference data was also performed. This showed less power than PLINK even
