I have about 300 differentially expressed genes for my data of STAR count. This is for two groups: treatment & control. However, for the same data consisting of all protein-coding genes, I don't get any gene set enriched significantly at FDR < 25%.
I am doing this with GSEA software for the hallmark of 50 gene sets. The parameters are in default. permutation type: phenotype.
Does anybody have any thoughts on why is this?
Is there anything that I am not doing correctly?