Hi, I am trying to run clusterProfiler::GSEA version 4.8.3 for each cluster of my SeuratObj
When ranking the DEG based on logFC I get decent ES/NES scores however my q/p values are usually > 0.05 sometimes even >0.5. However, when I re-run the code but use the area under the curve (auc) to rank my DEG I get way better NES and q/p values but worse ES scores.
Would appreciate your thoughts on this and which route would you suggest to follow.
library(clusterProfiler ) library(msigdbr ) m_t2g <-m_df<- msigdbr(species = "Mus musculus", category = "C7") %>% dplyr::select(gs_name, gene_symbol) %>% filter(grepl("DP|Tcell|TCELL|T_cell|THYMOCYTES|TH1|TH2|TH17|TCR|NKT", gs_name, ignore.case = TRUE)) markers <- wilcoxauc(SeuratObj, 'seurat_clusters') cluster_genes <- markers %>% filter(group == as.character(3)) %>% filter(padj <1) %>% arrange(desc(logFC)) %>% select(feature, logFC) ranks <- deframe(cluster_genes) rescp <- clusterProfiler::GSEA(ranks, TERM2GENE = m_t2g, eps = 0.0, minGSSize = 20, pvalueCutoff = 1)