I want to perform GSEA analysis on my DESeq2 results, but unfortunately, it does not work as it did (2 months ago), see error that follows after the code (at the bottom). I am 100% sure the data I am using is human. Do you know what causes this error?
Many thanks in advance!
Error: preparing geneSet collections... --> Expected input gene ID: BAX,KDM1A,VPS54,ENKUR,H2BC1,SLC19A1 Error in check_gene_id(geneList, geneSets) : --> No gene can be mapped....
#Order the genes from DESeq2 analysis (= res)
res.df <- as.data.frame(res)
res.df <- na.omit(res.df)
res.ordered <- res.df[order(-res.df$stat),]
gene_list_GSEA <- res.ordered$stat
#GSE analysis
gse <- gseGO(gene_list_GSEA,
ont ="ALL",
keyType = "SYMBOL",
OrgDb = "org.Hs.eg.db",
# nPerm = 10000,
minGSSize = 3,
maxGSSize = 800,
pvalueCutoff = 0.05,
verbose = TRUE
)