Of the four tools, only MAGMA and INRICH yield significant results after multiple testing correction (Tables 3 and 4). As with the self-contained gene-set analysis, power for the MAGMA analysis is better when using raw data rather than SNP p-values as input, though both yield one significant gene set. For INRICH the results are strongly dependent on the SNP p-value cut-off used, with three significant gene sets at the 0.0001 cut-off but none at the higher ones, further emphasizing the problem of choosing the correct cut-off. It should also be noted that the p-values have not been corrected for the fact that the gene-sets have been analysed under four different thresholds, and thus might not fall below the significance threshold if they were.
