What's the difference between enrichKEGG and gseKEGG

Question

[ben.kunfang]

Hi,

I was wondering what is the difference between enrichKEGG and gseKEGG in R package ClusterProfile. Thanks!

[ben.kunfang]

gseKEGG use the gene set enrichment analysis and enrichKEGG use over-representation test, and GESA doesn't need to run differential gene expression analysis beforehand

Answer 1

[h.mon]

Read Chapter 2 Functional Enrichment Analysis Methods, and then Chapter 6 KEGG analysis from the clusterProfiler online book.

[ben.kunfang]

Thanks, but I have to say I just don't like to way your answer. Yes, we can learn a lot by reading the help book, but what's the point I ask in the forum..I just want to save a little bit time to get a concise answer. Or otherwise why we need to go to school, we can just study at home by reading all the books.

[Kevin Blighe]

Hey, I do not see anything wrong with the answer by h.mon.. Remember that our communication channels here are electronic; so, things can be easily mis-interpreted. On Biostars, we are also volunteers and do not receive any payment for the time that we invest. Our expectation is that users who come here with questions have first invested their own time, exhaustively, in trying to resolve their problem(s).

[ben.kunfang]

I appreciate h.mon answer my question and I never say h.mon answer is wrong, I just say personally I don't like the way he answer. If you think answer a question by throwing a bunch of books is an appropriate way. That's fine. If you look my answer, don't you think it is more explicit than h.mon's? But it still need to invest time to learn what is gene set enrichment analysis and over-representation test. I never say the person who answer the question don't have to spend any time. I just hope the answer been more explicit instead of throwing the books.

[h.mon]

You are completely mixing up things: this forum is not school, and the volunteers here are not teachers. The main purpose of this site is to provide answers to well-formulated, well-explained specific questions. In particular, it is expected posters had already searched for a solution - did their homework, metaphorically speaking - so yes, we expect you to read the documentation before posting.

Please read the following posts about how to ask good questions in scientific forums:

[ Please read before posting a question ] -- How To Ask A Good Question

How To Ask Good Questions On Technical And Scientific Forums

[ben.kunfang]

Here is what I think, if you know the answer, you could answer the way Iike I answered.It doesn't need to type a lot of words and spend a lot of time. If you don't know the answer, you might giving the wrong books, so what's the point to give the help books? But still, I appreciated you answer my question, thanks a lot~

Answer 2

[liangqinsi]

From coding prospective:

enrichKEGG takes in only gene names, while gseKEGG takes in log2FC with gene names.

Why GSEA:

Gene Set Enrichment Analysis takes advantage of log2FC value, so the results are more informative and more accurate.

Answer 3

[Guangchuang Yu]

you should read the publication of clusterProfiler 4.0.

[liangqinsi]

clusterProfiler 4 rocks!

Answer 4

[youcai]

• enrichKEGG : over-representation analysis (ORA) using KEGG pathway
• gseKEGG : gene set enrichment analysis (GSEA) using KEGG pathway

data(geneList, package="DOSE")
## fold change > 2 as DE genes 
de <- names(geneList)[abs(geneList) > 2]

clusterProfiler 4.0.