If we use
same.dir = True in Gage, we got the following stats:
greater.p.geomean greater.stat.mean greater.p.val greater.q.val greater.set.size greater.exp1 less.p.geomean less.stat.mean less.p.val less.q.val less.set.size less.exp1 stats.stat.mean stats.exp1
If I want to pick the significant pathways, which qvalue I should use? For example, If it is significant in the less.q.val but not significant in the greater.q.val what does this mean? Is there any global pvalue to use?