Hello good people,

I have 4 conditions in my integrated single-cell dataset, each with paired pre- and post-treatment samples. For a specific cluster, I performed DEG analysis separately within each condition, for example:

CD4_condition1_pre vs CD4_condition1_post,

CD4_condition2_pre vs CD4_condition2_post,

CD4_condition3_pre vs CD4_condition3_post,

CD4_condition4_pre vs CD4_condition4_post,

Using the DEG results from each comparison, I performed over-representation analysis (ORA) and obtained pathway enrichment results. I then identified pathways that were significantly enriched and shared across conditions. Now, I would like to compare the fold enrichment values across these conditions for a specific pathway. However, I am concerned that directly comparing enrichment scores from separate ORA runs may not be statistically appropriate. What is the best way to perform this comparison in a valid manner? Like some normalization or scaling?