Clusterprofiler error: No gene can be mapped
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@tianshenbio-23283
Last seen 17 months ago

I am using the enricher function of clusterprofiler for GO enrichment of my non-model organism.

First I have my DE genes (n=638, converted as character):

gene <- read.csv("list.csv", header = F,sep=",")
gene <- as.character(gene[,1])
head(gene)
[1] "BANY.1.2.t20473" "BANY.1.2.t12787" "BANY.1.2.t10473" "BANY.1.2.t10472"
[5] "BANY.1.2.t08098" "BANY.1.2.t04432"

Then I have the term2gene

term2gene <- read.csv("GO2gene.csv",header=F,sep=",")
head(term2gene)
          V1               V2
1 GO:0002119  BANY.1.2.t15918
2 GO:0003916  BANY.1.2.t01379
3 GO:0005344  BANY.1.2.t10849
4 GO:0005344  BANY.1.2.t10852
5 GO:0005344  BANY.1.2.t10851
6 GO:0005344  BANY.1.2.t11738

and also term2name

erm2name <- read.csv("GO2name.csv",header=F,sep=",")
head(term2name)
          V1                                                       V2
1 GO:0000001                                mitochondrion inheritance
2 GO:0000002                         mitochondrial genome maintenance
3 GO:0000003                                             reproduction
4 GO:0000006    high-affinity zinc transmembrane transporter activity
5 GO:0000007 low-affinity zinc ion transmembrane transporter activity
6 GO:0000009                   alpha-1,6-mannosyltransferase activity

Then run the program

x <- enricher(gene,TERM2GENE=term2gene,TERM2NAME=term2name,pvalueCutoff = 0.05, pAdjustMethod = "BH",qvalueCutoff = 0.1)

Then I got:

--> No gene can be mapped....
--> Expected input gene ID:  BANY.1.2.t09827, BANY.1.2.t01112, BANY.1.2.t16389, BANY.1.2.t23551, BANY.1.2.t13938, BANY.1.2.t11911
--> return NULL...

What's the problem?

software error go annotation clusterProfiler • 224 views
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