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2 hours ago by

Hello. I am using clusterProfiler R package. I am trying to make a visualize result using a dotplot graph for my data.
It seems I am facing a stumbling block on the final analysis using compareCluster.
I am working with E. coliK12 strain and I want to perform an enrichment analysis with Kegg (enrichKEGG)
I wonder why my code is not working. The example of what I am trying to achieve is shown in this example link (yulab-smu.github.io/clusterProfiler-book/chapter11.html#formula-interface-of-comparecluster). Any ideas would be most appreciated. Thank you.

mydf <- data.frame(Entrez=names(geneQ), FC=geneQ)

head(mydf)

          Entrez       FC
    1    946671   7.1331936
    2    947072   5.7164422
    3    944863   5.4384038
    4    945322   3.8615915
    5    948027   3.7971514

mydf <- mydf[abs(mydf$FC) > 1,]

mydf$group <- "upregulated"

mydf$group[mydf$FC < 0] <- "downregulated"

mydf$othergroup <- "A"

mydf$othergroup[abs(mydf$FC) > 2] <- "B"

formula_res <- compareCluster(Entrez~group+othergroup, data=mydf, fun="enrichKEGG")

No enrichment found in any of gene cluster, please check your input...

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2 hours ago
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tpm10



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