I want to do functional analysis of RNAseq data. I noticed that two most famous approach "DAVID" and "GSEA" use very different way to do this. Thus, the pathways I obtained from them show little overlap.

Just want to ask, which one generally works better? Or both of them have their reason, it's just they have different preference in reporting pathways; then, I need to report pathways from both of them?

In addition, "DAVID" is based on differential expressed genes (DEGs). Will it be biased by the different methods I used to identify DEGs? For example, DESEQ2, EdgeR, or even t-test reports slightly different group of DEGs.