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tianshenbio
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@tianshenbio-23283
Last seen 4.9 years 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?
Cross-posted https://www.biostars.org/p/431270/
@dino game Thanks a lot for all.