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