Empty result using enrichGO
Hi Biostars,
I use clusterProfiler to do GO enrichment analysis, even though genes_to_test have 56 genes. The GO_results is empty. I am not sure why this happen. The same code worked well with down-regulated genes or with other res. Thank you so much for your help!
sigs <- na.omit(res)
sigs <- sigs[sigs$padj < 0.05 & sigs$baseMean > 50,]
genes_to_test <- rownames(sigs[sigs$log2FoldChange > 0.1,])
GO_results <- enrichGO(gene = genes_to_test, OrgDb = "org.Hs.eg.db", keyType = "ENSEMBL", ont = "BP")
as.data.frame(GO_results)
[1] ID Description GeneRatio BgRatio pvalue p.adjust qvalue geneID
[9] Count
<0 rows> (or 0-length row.names)
1 answer
No results are meeting the significance thresholds set by enrichGO.
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jared.andrews07
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