|Determining the contribution of gene weighting and moderated t-scores in PADOG when analyzing 229 KEGG metabolic and non-metabolic pathways|
The table shows statistics computed from nominal and adjusted p-values, and ranks of the 24 target pathways only, including geometric mean, median and percentages of pathways significant at 0.05 level based on nominal and adjusted p-values (q-values). The results of comparing the ranks of each method against noMnoW method, using a paired Wilcoxon test and a linear mixed-effects model, are included. The best value for each criterion is shown in bold. PADOG is compared against simpler approaches that i) use gene weights but regular rather than moderated t-scores (noM), ii) use moderated t-scores but no gene weights (noW) and iii) use neither moderated t-scores nor gene weights (noMnoW).
Tarca et al.
Tarca et al. BMC Bioinformatics 2012 13:136 doi:10.1186/1471-2105-13-136