clusterProfiler - enrichGO and enrichPathway not returning any results
Entering edit mode
Last seen 4.9 years ago
United States

I'm attempting to run some gene ontology analysis as well as pathway analysis using the Reactome database, but i'm running into something interesting.

I'm not returning any results. So whenever I go to visualize my data using a dotplot, it returns an empty image. What am I doing wrong?

File is a 6 column typical bed format. Data is in hg19.

data <- readPeakFile($bed)

gene <- seq2gene(data, tssRegion = c(-1000,1000), flankDistance = 3000, TxDb = txdb)

reactome <- enrichPathway(gene)

head(gene, 2)

[1] ID   Description   GeneRatio   BgRatio   pvalue   p.adjust   qvalue   geneID

[9] Count

<0 rows> (or 0-length row.names)

Is this potentially just a result of not having any enriched Pathways? I get a similar problem when I try to use `enrichGO`.


Thank you.

clusterProfiler • 1.5k views
Entering edit mode

- What is the actual output of head(gene, 2)? It is certainly not what you show here.... Please also note that gene should be a character vector of  EntrezIDs.

- What happens if you include the argument pvalueCutoff = 1 with enrichPathway(gene)? Maybe you don't have any significant results using the default cutoff value of FDR <0.05.


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