Selecting DEGs for gene ontology using clusterprofiler and DESeq2

Question

[a.basitkhan1990]

Hi all,

I am using DESeq2 to generate a DEG list and then feeding significant genes into enrichGO function of clusterprofiler (using below code).

My question is if there are any standard definitions of what constitutes a "significant" gene for GO analysis on the basis of L2FC, padj, basemean, etc.

Thanks much!

res<-results(dds)
sigs<-na.omit(res)
sigs<-sigs[sigs$padj < 0.05 & sigs$baseMean >50,]
sigspos<-sigs[sigs$log2FoldChange>0,]
sigsposname<-sigspos$symbol
sigsneg<-sigs[sigs$log2FoldChange< 0,]
sigsnegname<-sigsneg$symbol

SZup<- enrichGO(gene = sigsposname, OrgDb = "org.Hs.eg.db", keyType ="SYMBOL", ont = "BP")

[Ming Tommy Tang]

depends on your results. typically padj <=0.05, abs(logFC)>=1

[a.basitkhan1990]

Thank you!

[a.basitkhan1990]

Would greatly appreciate any help!!