No gene can be mapped

Question

[yang.zhizhang]

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.

[jv]

My dataset 's gene id is ENSG... what would be wrong?

maybe double check that your gene ids don't have any trailing or leading whitespace?

one option would be str_trim from stringr https://stringr.tidyverse.org/reference/str_trim.html

[seidel]

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

[yang.zhizhang]

[jv]

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.