In February I made a GSEA analysis using Clusterprofiler and WIkipathways and I got my results of pathways that are sign. enriched (p-adjusted0.05) in each of the conditions.. I wanted to confirm my results before publishing and re run the code recently. Everything is the same except 3 pathways do not come up anymore ( estrogen receptor pathway and two eicosanoid metabolism pathways) in any of the conditions it showed previously. Even if I ask to have all pathways enriched (put the pvalueCutoff=1) they do not appear. Which leads me to think that it is not they are not significant but something in the package perhaps changed? If I use the online tool Webgestalt and the same exact list the 3 pathways show up again ... Is there any explanation for three pathways suddenly not being considered by GSEA?