I want to run GSEA on my scRNA-seq data using cluster markers. I want to compare enrichment scores for gene sets and pathways across clusters in my data. I used Seurat FindAllMarkers to find DEGs for each cluster (cluster of interest vs all remaining cells). For GSEA, I want to use only DEGs with adj p-value < 0.05. As GSEA takes expression data as input, I need to find average expressions of significant DEGs per cluster and make a txt file with counts for each gene across the clusters.
But as I am dealing with DEGs, they will be different for each cluster. How should I impute data for those DEGs which are significant for cluster A but not significantly differentially expressed in cluster B (but still somehow expressed)?