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Question: GSEA using clusterProfiler
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gravatar for giuseppe0525
7 days ago by
giuseppe05250 wrote:

Hello, everyone

I 'm working on GSEA using clusterProfiler​ and came across two problems.

1. How should I prepare geneList​

2. What does TERM2GENE mean​?

I've worked out the differentially expressed genes from mouse microarray data.

Then I tried the following script but failed to obtain the results.

"

library(clusterProfiler)

geneList <- results$gene.id
geneList <- levels(geneList)
geneList = sort(geneList, decreasing = TRUE)
head(geneList)


term <- rep("ischemia24h",length.out = 844)
head(term)

TERM2GENE <- cbind(term, geneList)
head(TERM2GENE)

GSEA(geneList,
     exponent = 1,
     nPerm = 1000,
     minGSSize = 2,
     maxGSSize = 5000,
     pvalueCutoff = 0.05,
     pAdjustMethod = "BH",
     TERM2GENE,
     TERM2NAME = NA,
     verbose = TRUE,
     seed = FALSE,
     by = "fgsea")

"

##

preparing geneSet collections...
--> Expected input gene ID: 94094,223650,17926,12831,29875,68178
Error in check_gene_id(geneList, geneSets) : 
  --> No gene can be mapped....

 

Thank you!

 

 

ADD COMMENTlink written 7 days ago by giuseppe05250
1

Hi,

It seems that you have the same issue as in your previous question regarding clusterProfiler. Have you checked that your supplied gene list of the right type and from the right species? It would be helpful if you also showed the output of the function:

>head(geneList)

Regarding the TERM2GENE I found this section in the vignette to the package:

"TERM2GENE is a data.frame with first column of term ID and second column of corresponding mapped gene and TERM2NAME is a data.frame with first column of term ID and second column of corresponding term name. TERM2NAME is optional."

ADD REPLYlink written 7 days ago by thokall60
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