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?
Without having access to all your input files it is difficult to explain why this happened. However, some thoughts... Did you use the exact same version of R and Bioconductor packages as in February?
Thus:
clusterProfileruses entrez ids as central input identifiers, and if the mapping entrez id <-> ensembl id has changed, this may result in having less than 10 genes mapped to the ER pathway.... See also my 1st comment.