described above, n = 7 and m = 6 for i-GSEA, while n = 2 and m = 2 for GSEA. Further comparison by using the other six Wellcome Trust Case Control Consortium GWASs except bipolar disorder (2) obtained the result that n = 33 and m = 14 for i-GSEA, while n = 2, m = 1 for GSEA. In addition, the pathways identified (FDR < 0.05) by i-GSEA include all the pathways identified by GSEA in all the above comparisons. These show that i-GSEA has improved sensitivity in comparison to GSEA. Our data examples also show that i-GSEA4GWAS obtains very meaningful results with different GWAS designs (quantitative trait and case/control) and different genotyping platforms (Illumina and Affymetrix).
