No gene can be mapped in enrichGO function

[shiyi-pan]

Hi, I want to clusterProfiler to do GO enrich analysis. First , I use AnnotationForge to create the Orgdb package because it's non-model specie. It works well. Then I use enrichGO to do GO enrich analysis and find "No gene can be mapped". Here is my genes:

NN03g01177.1 NN08g01881.1 NN15g00474.1 NN08g02566.1

here is my script:

""" gene <- read.table(file = "test_degs.txt",header = T)

de_ego <- enrichGO(gene = gene, OrgDb = org.Gm.eg.db, keyType = "GID", ont = "BP", qvalueCutoff = 0.05, pvalueCutoff = 0.05)

"""

Here is the results:

--> No gene can be mapped.... --> Expected input gene ID: NN06g00399.1,NN13g00022.1,NN17g00152.1,NN15g02698.1,NN10g01422.1,NN11g01444.1 --> return NULL... Warning message: call dbDisconnect() when finished working with a connection

Could you give me how to fix it ? Thank you very much.

[alexwu66666]

gene <- read.delim('file', sep = '\t', check.names=FALSE) gene <- gene[,1]

hope it works.

[shiyi-pan]

Thank you for your reply. It works.

[Pedramto89]

When I want to run this: gse <- gseGO(geneList=gene_list, ont ="ALL", keyType = "SYMBOL", nPerm = 1000, minGSSize = 3, maxGSSize = 800, pvalueCutoff = 0.05, verbose = TRUE, OrgDb = organism, pAdjustMethod = "BH")

I get this error: "preparing geneSet collections... --> Expected input gene ID: GALNT3,TFPT,VIP,TAF1L,FAM209A,MEIKIN Error in check_gene_id(geneList, geneSets) : --> No gene can be mapped...."