Guido Hooiveld

So it seems your problem is not directly related to `enrichplot`... Yet, it is not clear to me what exactly you try to achieve. To increase your chance of getting...

I realize that you updated this thread few weeks ago, but I hope my reply is still useful. It looks to me that you forgot to include the `merge_result` step......

Thanks for having a look at this discrepancy, and finding and fixing the source of it so quickly. :) Since processing of files on the `AnnotationHub` apparently may take some...

Thanks for the updated file. I have downloaded it, and based on my tests it looks fine now. That is, **all** my input genes (63086) are being annotated now (in...

Also obtained expected results on the level of transcripts, so as far as I am concerned the updated database is correct. @zyh4482 : what about the outcomes of your analyses?

For the archive: this issue has been cross-posted/discussed at the GitHub of `fgsea`: https://github.com/ctlab/fgsea/issues/154

What is the output from: `tail( as.data.frame(kk) )`

Aha, that suggests the significance filtering indeed worked. Please be aware that: - false discovery rates (FDR) can be calculated according to multiple procedures. - Benjamini and Hochberg (BH) were...

Yes, it is expected that results between 2 runs are slightly different. Note that `clusterProfiler` uses under the hood the function `fgseaMultilevel` (from the package `fgsea`) for GSEA-based analysis. The...

I agree that this is not (very well) documented. According to the help page of `dotplot` (`?dotplot`), the default setting of the argument `size` is `NULL`. If needed, it can...