No gene can be mapped with gsePathway

[alexandrafleming]

Hello,

I am trying to run reactomePA for my DE genes. I manage to run enrichPathway successfully (yy = enrichPathway(genes$entrezgene_id, pvalueCutoff=0.05)),
but when I do the following:

sorted_genes = sort(genes$entrezgene_id, decreasing = TRUE)
gseP = gsePathway(sorted_genes, organism = "human", pvalueCutoff = 0.05, pAdjustMethod = "BH", verbose = TRUE)

I am getting this error:

preparing geneSet collections...
--> Expected input gene ID: 1072,2768,3804,3479,3659,5742
Error in check_gene_id(geneList, geneSets) :
--> No gene can be mapped....

What could cause this issue?

Also the reactomePA manual page is not available: https://guangchuangyu.github.io/ReactomePA/ Is there somewhere else the manual?
And a last question: Could I run the reactomePA analysis with my background set of genes?

Thank you in advance!
Kind regards,
Alex

[DrDaedalusWHU]

I think the ReactomePA manual is here. Please check Chapter9: Reactome enrichment. https://yulab-smu.top/biomedical-knowledge-mining-book/reactomepa.html

[alexandrafleming]

Thank you for you reply.