Guido Hooiveld

Please note that you misinterpreted what `groupGO` is doing, and therefore you should achieve your goal slightly different! Having said this, regarding the error: reason for it is that the...

Does it work with the example code (since your code as such is not reproducible)? What is your `sessionInfo()`? ``` > library(clusterProfiler) > data(gcSample) > xx xx # # Result...

You should provide more information on your R/Bioconductor installation! Are you sure it is up-to-date? That is, using `R-4.3.x` and `Bioconductor 3.18`? There have been changes in the KEGG API...

Happy to hear you got it _somehow_ working, but to show for the record/archive that` compareCluster` also works with the generic function `enricher`: ``` > library(clusterProfiler) > > ## load...

As said, AFAIK recently (a couple of months ago) there have been some issues with connecting to the KEGG API. These have been addressed, so I strongly recommend you update...

Nice to hear it is working for you now!, but... the `KEGG_DATA` object would normally not be required, except if there are problems connecting to the online KEGG site/database. Could...

Apparently this seems not to be possible, because of the lack of support to do this in `topGO`. See: https://support.bioconductor.org/p/89014/

FYI: it is working fine for me when using the latest version of R/Bioconductor: @lizhan96 : ``` > library(clusterProfiler) > > ## use your first 18 genes as sample input...

Note that I am not an expert on metabolomics. Yet, my thoughts: by using the generic functions `enricher` and `GSEA` one could perform over-representations resp. enrichment analysis on _any_ type...

Please use the latest version of R (=R-4.3.x) and Bioconductor (=3.18)! Development of packages goes on continuously, and you are using a very old version of R (and corresponding Bioconductor...