I am performing pathway analysis using results from RNA seq. I am using clusterprofileR from R and using the KEGG pathway. I obtained two sets of results using
gseKEGG(geneList = my_gene_list, organism = kegg_organism, nPerm = 50000, minGSSize = 3, maxGSSize = 800, pvalueCutoff = 0.05, pAdjustMethod = "none", keyType = "ncbi-geneid")
my_gene_list was filtered list of top ~400 genes with the highest log2fold change
my_gene_list was the entire gene list ~18K sorted based on log2fold change value.
I was expecting both methods to list the same set of pathways as top activated/suppressed pathways but method one gives me some pathways of interest as top list while the results from method 2 look mostly garbage. How do I interpret results from both of these approach?