TransWikia.com

GSEA: unable to find an inherited method for function ‘keytypes’ for signature ‘"standardGeneric"’

Geographic Information Systems Asked by tadage on August 16, 2021

I can’t understand this problem. Even when I use the data and code offered at https://learn.gencore.bio.nyu.edu/rna-seq-analysis/gene-set-enrichment-analysis/ , the problem also existed.

enter image description here

I did the analysis follow the official illustrate. As bellows:

library(clusterProfiler)
library(enrichplot)
library(ggplot2)
library(org.Dm.eg.db)
library(DOSE)
library(biomaRt)

df = read.csv("~/lineagepaper/drosphila_example_de.csv", header=TRUE)

original_gene_list <- df$log2FoldChange

names(original_gene_list) <- df$X

gene_list<-na.omit(original_gene_list)

gene_list = sort(gene_list, decreasing = TRUE)
head(gene_list)

enter image description here

gse <- gseGO(geneList=gene_list, 
             ont ="ALL", 
             keyType = "ENSEMBL", 
             nPerm = 10000, 
             minGSSize = 3, 
             maxGSSize = 800, 
             pvalueCutoff = 0.05, 
             verbose = TRUE, 
             OrgDb = organism, 
             pAdjustMethod = "none")

enter image description here

One Answer

I just ran into the same problem while working with the same tutorial and solved it this way . So the argument OrgDb doesn't take in "org.Hs.eg.db" which is a string. Instead , put in the name of the annotation database directly for that argument.

Example:

gse <- gseGO(geneList=gene_list, 
             ont ="ALL", 
             keyType = "SYMBOL", 
             nPerm = 10000, 
             minGSSize = 3, 
             pvalueCutoff = 0.05, 
             verbose = TRUE, 
             OrgDb = org.Hs.eg.db, 
             pAdjustMethod = "none")

Answered by user188544 on August 16, 2021

Add your own answers!

Ask a Question

Get help from others!

© 2024 TransWikia.com. All rights reserved. Sites we Love: PCI Database, UKBizDB, Menu Kuliner, Sharing RPP