This is a test version of Biostars. For the public version, visit https://www.biostars.org.
No gene can be mapped

Hi

When I do my data's Gene Set Enrichment Analysis with ClusterProfiler using codes of Mohammed Khalfan from website, when I run the following code and got the error message.

gse <- gseGO(geneList=gene_list, 
             ont = "ALL",
             keyType = "ENSEMBL", 
             nPerm = 10000, 
             minGSSize = 3, 
             maxGSSize = 800, 
             pvalueCutoff = 0.05, 
             verbose = TRUE, 
             OrgDb = organism, 
             pAdjustMethod = "none")

preparing geneSet collections...

    --> Expected input gene ID: ENSG00000157404, ENSG00000185650, ENSG00000106410, ENSG00000143569, ENSG00000102904, ENSG00000125686
    Error in check_gene_id(geneList, geneSets) : 
      --> No gene can be mapped....

My dataset 's gene id is ENSG... what would be wrong? I set organism code below:

organism = "org.Hs.eg.db"
BiocManager::install(organism, character.only = TRUE)
library(organism, character.only = TRUE)

I am new to R and really appreciate your help.

r gsea
• 5,674 views • link
updated by jv jv • written by yang.zhizhang • yang.zhizhang

Show us the result of: head(gene_list) to see if your gene list is in the right format.

• 0 views • link
written by seidel seidel

that looks like an excel spreadsheet and not the actual gene_list object from your code which doesn't help troubleshoot

It would help greatly if you showed the code you used to create gene_list the file shown in your screenshot.

• 0 views • link
written by jv jv

0 answers

No answers yet.

Log in to answer this question.

More posts like this