Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

"No gene can be mapped" when running enrichPathway #24

Open
RuiyangLiu94 opened this issue Jan 23, 2020 · 4 comments
Open

"No gene can be mapped" when running enrichPathway #24

RuiyangLiu94 opened this issue Jan 23, 2020 · 4 comments

Comments

@RuiyangLiu94
Copy link

Hi,

Thanks for establishing the R-based Reactome tool.

I want to do a pathway analysis based on a list of mouse genes, but when I tried the function enrichPathway, an error pops out as
"--> No gene can be mapped....
--> Expected input gene ID: 5660,5695,23295,25915,161,3433
--> return NULL..."

I used the entrez id associated with the geneset as the function input; I also tried to upload this entrez id list to Reactome website for analysis. For the web-based analysis, there are some results popping out. Therefore I am wondering what could be the reason for the error? Is it because no pathways are found or because the entrez id from mouse are not accepted by ReactomePA?

for reference the code I used to run pathway analysis is:
x <- enrichPathway(gene=geneset_entrez,pvalueCutoff=1, readable=T)

Looking forward to your reply!

Ruiyang

@Cpp-maker233
Copy link

https://www.biostars.org/p/431270/#481056.I see this error ion Biostars with this link ,I havent solved this error yet and hope it can help us

@GuangchuangYu
Copy link
Member

we can't help without reproducible example

@Cpp-maker233
Copy link

Cpp-maker233 commented May 7, 2021 via email

@AiweiWu
Copy link

AiweiWu commented Feb 28, 2023

The same error when I run enrichKEGG.

genesets
[1] "27395" "18777" "21399" "108664" "12421" "654788"
eKEGG <- enrichKEGG(genesets, organism = "mmu",pvalueCutoff = 0.05, keyType = 'kegg')
--> No gene can be mapped....
--> Expected input gene ID:
--> return NULL...

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

4 participants