how to compare different conditions

[Flu09]

hello,

I have run Seurat's findmarkers to compare between genotype1 diseased versus healthy celltypes
then between genotype2 diseased versus healthy celltypes

then I used gseGO() to find the pathways for each celltype

I always found too many ES > 0 (upregulated) and few or zero with ES <0 (downregulated)
Is this normal for gseGO since we use all gene and do not filter by pvalue or logfc?

Now I am wondering how to compare the output since mostly they are redundant pathways and similar or the same but different in rank or padj, how to compare the results and aggregate them