Hi Everyone !!
With my first post this year, I wish the best for everyone !!
Coming to the confusion, I have analyzed RNASeq data of leukemia with 2 conditions (one with Loss of Heterogeneity and one without it, 14 samples to each conditions). Now I made 3 gene sets based on different pathways and functions. These gene sets had quite a few genes in common.
After I ran GSEA on these gene sets (separately) I found that genes like FOSB, ATF3, MYC they are enriched in one analysis (done with Gene set 1) while non-enriched in another analysis (done with Gene set 2) while I gave the same expression sheet, same metadata(cls file)
Q.1> when is this possible ??
Q.2> some of these genes were down regulated in DGE for LOH condition but shows enrichment in GSEAnalysis. How do we explain this ?
Thanks and Regards