I keep getting this Error message:
preparing geneSet collections... --> Expected input gene ID: C9orf78,CNOT9,SPIDR,FAM9B,SDC1,CCDC182 Error in check_gene_id(geneList, geneSets) : --> No gene can be mapped....
Here is my code, i attempting to perform gene set enrichement analysis:
GroupA <- results(dds, name = "Cancer_Type_healthy_vs_MESO") original_gene_list <- GroupA$log2FoldChange names(original_gene_list) <- GroupA$X gene_list<-na.omit(original_gene_list) gene_list = sort(gene_list, decreasing = TRUE)
gse <- gseGO(geneList=gene_list, ont ="ALL", keyType = "SYMBOL", nPerm = 10000, minGSSize = 3, maxGSSize = 800, pvalueCutoff = 0.05, verbose = TRUE, OrgDb = org.Hs.eg.db, pAdjustMethod = "none")
Please can someone tell me what is wrong with my code?
You need to show an example of your list