Question: genlist for clusterprofiler
gravatar for archie
9 days ago by
archie40 wrote:

Dear all,

I am using the clusterprofiler. I used the enrichGO, enrichKEGG and enrichDO .

data<-read.delim("enrich.txt") genes<-data$entrez[abs(data$expr)>2]

I used genes as input in enrichGO,enirchKEGG. But I am not able to create input geneList for the gse function .

ego3 <- gseGO(geneList = geneList, OrgDb =, ont = "CC", nPerm = 1000, minGSSize = 100, maxGSSize = 500, pvalueCutoff = 0.05, verbose = FALSE) I have gene list with log2fold change. Therefore I also want to analyse ontology based on the gene set enrichment gseGO and gseKEGG functions.

Can anybody suggest me how to prepare this input file from tab seprated data file.

All suggestions will be appreciated.

Thank you

clusterprofiler • 76 views
ADD COMMENTlink modified 9 days ago by Guangchuang Yu1.7k • written 9 days ago by archie40
gravatar for Guangchuang Yu
9 days ago by
Guangchuang Yu1.7k
China/Hong Kong/The University of Hong Kong
Guangchuang Yu1.7k wrote:

see the tutorial on

ADD COMMENTlink written 9 days ago by Guangchuang Yu1.7k
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