"compareCluster with enrichGO" gives me NA for one of the conditions

[Guerande29]

Cheers, I have differentially expressed genes for three conditions (3, 6 and 10 DAS). I do the cluster comparison using "enrichGO". For the Upregulated comparison it works very well, but for the downregulated comparisons NA appears for 3 DAS; I think this is not right; Although I don't know how to explain it. pdta: Previously it happened to me with other data, but at that time it was just my essays and I didn't pay attention.

Is there any idea for this?

Thank you very much

I had 193 DEGs at 3 DAS 7158 DEGs at 6 DAS 3598 DEGs at 10 DAS

RStudio 2022.02.2+485 "Prairie Trillium" Release (8acbd38b0d4ca3c86c570cf4112a8180c48cc6fb, 2022-04-19) for Windows Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36

This is my script

#Librarys library(clusterProfiler)
library(org.At.tair.db)
library(forcats)
library(enrichplot)
library(pathview) library(data.table)
library(ggplot2)
library(GOsummaries) library(DOSE)
library(reshape)

#Comparison Dowm Regulated at 3, 6 and 10 DAS

setwd("D:/cpaA_cpaH2O")

universe<- read.delim ("Universe.txt") universe<-as.character(universe[,1]) universe <- sort(universe, decreasing = TRUE)

#File DEG_Downgrupos = read.delim("ComparisonDown.txt", header = TRUE)

#change names names(DEG_Downgrupos) DEG_Downgrupos = rename(DEG_Downgrupos, c(Down_3DAS = "3 DAS" , Down_6DAS = "6 DAS" , Down_10DAS = "10 DAS"))

#Checking change View(DEG_Downgrupos)

#ORA with Clusterprofiler ORA_Downgrupos <- compareCluster(geneClusters=DEG_Downgrupos,enrichGO, OrgDb = org.At.tair.db, keyType = "TAIR", ont = "BP", pAdjustMethod = "BH", universe = universe, pvalueCutoff = 0.05, qvalueCutoff = 0.05, readable = FALSE)

clust_result<-as.data.table(ORA_Downgrupos) tapply(clust_result$Cluster,clust_result$Cluster,length)

---

> tapply(clust_result$Cluster,clust_result$Cluster,length) 3 DAS 6 DAS 10 DAS NA 178 205

###############SO, I tried to do the GO analysis only for 3DAS and the same thing happens, there are result, but when I applied "simplify" the result does not associate any GO term. Check the data, I don't find anything strange...

Is there any idea for this?

Thank you very much