Actually, I put the DEG list directly to PANTHER that resulted in the GO or pathway analysis data. However, I want to use GSEA.
Meanwhile, I found nice online site and follow their codes for the GSEA analysis(https://bioinformaticsbreakdown.com/how-to-gsea/).
And, here is the my code.
tmp = read.csv("/data/directory/DEGs_HCvsJSS_DC.csv", header = TRUE) %>% filter(Gene.Symbol !="") GO_file = "/blue/zhangw/my.kim/HCvsJSS/c5.all.v7.4.symbols.gmt" # got this from http://www.gsea-msigdb.org/gsea/msigdb/collections.jsp gene_list = tmp$avg_log2FC names(gene_list) = tmp$Gene.Symbol gene_list = sort(gene_list, decreasing = TRUE) gene_list = gene_list[!duplicated(names(gene_list))] head(gene_list) res = GSEA(gene_list, GO_file, pval = 0.05) # this caused the error as follows. Error in build_Anno(TERM2GENE, TERM2NAME) : argument "TERM2GENE" is missing, with no default
It's really dissapointing because I found this relatively easy protocol for GSEA, but found the error, lol.
Do you guys have any suggests for this troubles? or any recommendations for GSEA analysis that can be done with DEG list generated from seruat scRNAseq data?