-
Notifications
You must be signed in to change notification settings - Fork 254
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
How to run enrichment analysis of metabolites using clusterProfier #731
Comments
A pointer is given in, for example, the protocol recently published in Nature Methods, See section 1.9 on page 16. In essence you can use the
|
I tried to run this using a set of compound IDs, and I got an error. I also get the same error using your example code. , but if I run enrichKEGG using gene ID, it works fine, suggesting that the KEGG website is okay, but the cpd IDs don't map. keggChem [1:13] kk <- enrichKEGG(gene = keggChem[1:10], Error in content[, 1] : subscript out of bounds |
Hello @lungboyz - thanks for sharing. Would it be possible to share an both - example with error , and the example that worked, so its easier to compare and understand ? Much appreciated |
When using your 13 input ids it is working for me.... For testing purposes I would set all significance cutoffs to 1 (like I do below; so that no filtering is occurring). You also may need to use the latest version of
|
I have a list of metabolites, In the form of metabolite names, and also in the form of KEGG Ids. How can i run enrichment analysis on this data ? Please advise
Example data:
The text was updated successfully, but these errors were encountered: