Question

cnetplot with enrichKEGG results

0

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fatimaruizdelabastida ▴ 10

@5215d925

Last seen 3.0 years ago

Spain

Hello! I'm trying to use cnetplot function with a KEGG enrichment object obtained from enrichKEGG function. However, I get the same error and I don't know how to solve it. I'm using clusterProfiler package to perform this analysis.

I provide the code to reproduce the data:

# KEGG enrichment of two specific genes:
aa = enrichKEGG(c(5104, 94025))

# plot the results with cnetplot:
cnetplot(aa)

## Error in UseMethod("rescale") : 
## no applicable method for 'rescale' applied to an object of class "AsIs"

sessionInfo( )
## R version 4.1.1 (2021-08-10)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 11.6

Thanks in advance!

clusterProfiler enrichKEGG cnetplot • 4.3k views

ADD COMMENT • link 3.1 years ago fatimaruizdelabastida ▴ 10

1

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Mmm, to be honest, using only 2 genes for KEGG overrepresentation analysis does not really make sense to me.... but I think the error is due to the fact that only 1 of your 2 input genes is mapped to a KEGG pathway, and therefore scaling of expression values is not possible. (FYI only gene 5104 is annotated in the KEGG database).

If you have at least 2 genes that are mapped, it works....!

> data(geneList, package='DOSE')
> de2 <- names(geneList)[1:2]
> yy2 <- enrichKEGG(de2)
> 
> cnetplot(yy2)

... but if only a single gene is mapped, it doesn't work! I got the same error as you got, that implies that scaling didn't work (which indeed is not possible with only 1 gene).

> de1 <- names(geneList)[1]
> yy1 <- enrichKEGG(de1)
> 
> cnetplot(yy1)
Error in UseMethod("rescale") : 
  no applicable method for 'rescale' applied to an object of class "AsIs"
>

ADD REPLY • link 3.1 years ago Guido Hooiveld ★ 4.1k

0

Entering edit mode

Thank you so much! It's true it doesn't make sense to perform an enrichment with only two genes, but since I want to develop a pipeline for my lab, I want to overcome all possible cases.

Thanks again!!

ADD REPLY • link 3.1 years ago fatimaruizdelabastida ▴ 10