Im doing GSEA with the clusterProfiler package in R, and I have a question about direction. When Ive done gsea on other platforms there was a column saying whether the gene set was "up" or "down." I don't see this in the gsearesult object. So if the gene set GSE23321_CENTRAL_MEMORY_VS_NAIVE_CD8_TCELL_DN is in the result is that saying genes that are down regulated in memory t-cells vs naive are upregulated in mine or also down regulated?
It is a bit complex to explain enrichment as up/down and neutral. I would say that the genes you have are positively / negatively enriched in up-regulated direction and/or exact opposite for down-regulated genes.
In fact, I have tried to cope with pathway enrichment issue before and our team could not solve it how we should exactly interpret the result.