I've recently started using topGO in my expression analysis and like it a lot. The "elimination" paradigm is a very useful one when doing pathway analysis, since many different pathways do in fact overlap in the genes they contain.
In the manual, all the examples are using p-values as a statistic, but never separate the up- and down-regulated genes. They should be considered separately, should they not?
And, correspondingly, would it be necessary to modify the application for Kolmogorov-Smirnov statistic and KS-elim? In classical GSEA, your statistic has a plus or a minus sign, to indicate if the gene is up- or down-regulated. However, since you're only using the p-values, I was curious as to how can you separate them.
Additionally, it would be nice to understand how are the p-values used in Kolmogorov-Smoirnov (like) methods in topGO, and whether it is possible to use another statistic - such as t-statistic from limma or Wald statistic from DESeq2.