Empty result using enrichGO

Question

[Chris]

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)

Answer 1

[jared.andrews07]

No results are meeting the significance thresholds set by enrichGO.