Question: Clusterprofiler error: No gene can be mapped
0
gravatar for tianshenbio
7 months ago by
tianshenbio70
tianshenbio70 wrote:

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:

term2name <- 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 it:

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

And I got this...

--> 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...

Everything seems fine so I really hope to know what the problem is, thank you.

ADD COMMENTlink modified 6 months ago by Biostar ♦♦ 20 • written 7 months ago by tianshenbio70

Are these gene identifiers official gene symbols? Is your species supported by the tool?

ADD REPLYlink written 7 months ago by ATpoint41k

No, they are not, thats why I used enricher since that's for my customized datasets

ADD REPLYlink written 7 months ago by tianshenbio70
2
gravatar for MatthewP
7 months ago by
MatthewP800
China
MatthewP800 wrote:

Hello, can you run intersect(term2gene$V2, gene) ? Maybe no gene hit by any pathway.

ADD COMMENTlink written 7 months ago by MatthewP800

Hi, it shows character(0)...But I searched several genes manually and they did exist in term2gene$V2, what could be the problem?

ADD REPLYlink modified 7 months ago • written 7 months ago by tianshenbio70
2

Maybe try print(head(term2gene$V2), quote=TRUE) to see whether maybe some spaces around your string.

ADD REPLYlink written 7 months ago by MatthewP800

You are right...a space ahead of each term...

print(head(term2gene$V2), quote=TRUE)
[1] " BANY.1.2.t15918" " BANY.1.2.t01379" " BANY.1.2.t10849" " BANY.1.2.t10852"
[5] " BANY.1.2.t10851" " BANY.1.2.t11738"
ADD REPLYlink modified 7 months ago • written 7 months ago by tianshenbio70

This solved it?

ADD REPLYlink written 6 months ago by Kevin Blighe67k
1

Yes, space was introduced in front of each term, when I removed it everything went well!

ADD REPLYlink written 6 months ago by tianshenbio70
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