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12 months ago

So I have a list of DE genes that I would like to analyse for enriched GO and KEGG terms. I was going to use clusterProfiler for this, but I can't seem to get past constructing the gene list. I have followed the vignette and I believe that I have constructed my gene list correctly as a sorted named vector of Entrez IDs, but it still doesn't work. Below is the output of the sample gene list in the vignette and my list. There appears to be no difference between my named vector and the example, yet the example works and mine does not.

> str(geneList) # example gene list in vignette
Named num [1:12495] 4.57 4.51 4.42 4.14 3.88 ...
- attr(*, "names")= chr [1:12495] "4312" "8318" "10874" "55143" ...

> str(gene_list) # my gene list that I have constructed
Named num [1:18907] 4.64 4.25 3.89 3.64 3.5 ...
- attr(*, "names")= chr [1:18907] "13048" "100043108" "13099" "23850" ...


I get the following error when I run

de <- names(geneList)[abs(gene_list) > 2]
edo <- enrichDGN(de)

--> No gene can be mapped....
--> Expected input gene ID: 229,151393,5076,2006,3622,8302
--> return NULL...

gsea software error clusterProfiler • 544 views
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Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (text becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

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enrichDGN only supports human genes, and I guess your gene list is from other species.

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Correct. I realized that my data was for mouse. The clusterProfiler vignette does not make it abundantly clear that it is only for human.