I am a bit confused by these two methods.
By definition, gene set enrichment analysis (GSEA) uses a priori gene sets that have been grouped together by their involvement in the same biological pathway. This seems the same as how pathway analysis choose the predefined gene list (by pathway). Can anyone eliberate any differences between this two methods.
I know that GSEA use 'signature' to represent specific biological process while other resources like panther or GO enrichment analysis may uses different gene set to represent the same biological process. Would this cause conflict? Different tools may get different results from the same input gene set.