RuiyangLiu94 commented 4 years ago

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 commented 3 years ago

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 commented 3 years ago

we can't help without reproducible example

Cpp-maker233 commented 3 years ago

I'm very sorry I can not slove this problem because mine is not sloving till now.

------------------ 原始邮件 ------------------ 发件人: @.>; 发送时间: 2021年5月5日(星期三) 凌晨5:05 收件人: @.>; 抄送: @.>; @.>; 主题: Re: [YuLab-SMU/ReactomePA] "No gene can be mapped" when running enrichPathway (#24)

Hello,

I have a similar issue.

Here's the code I ran. I upped the p-value cut off super high, just to see if I'd get anything.

diff_genes_list = list.files(pattern="LocusLinkIDs-*") diff_genes_list

all_genes <- read.csv(diff_genes_list[1],header = TRUE)

Removed gene IDs not having the TAIR format

for (m in c(2:4)) {

diff_genes = read.csv(diff_genes_list[m],header = TRUE)

GO_analysis <- enrichGO(gene = diff_genes, universe = all_genes, OrgDb = org.At.tair.db, # contains the TAIR/Ensembl id to GO correspondence for A. thaliana keyType = "TAIR", ont = "ALL", # either "BP", "CC" or "MF", pAdjustMethod = "BH", qvalueCutoff = 1, #0.05, readable = TRUE, pool = TRUE)

GO_analysis

}

Attached is one of the deferentially expressed gene files and the list of all possible genes for the 'universe'. LocusLinkIDs-all.txt LocusLinkIDs-lightcyan.txt

I'd love some help!

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AiweiWu commented 1 year ago

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...

YuLab-SMU / ReactomePA

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

Removed gene IDs not having the TAIR format