ERROR in enrichGO,when seting ont = "ALL",Error in data.frame(..., check.names = FALSE) : 行名里有缺失值。

[XIANZHE-LI]

go <- enrichGO(gene = id,
#universe = names(geneList),#背景基因
OrgDb = "org.Mm.eg.db",
ont = "ALL",#"BP", "MF", "CC"
pAdjustMethod = "BH",
pvalueCutoff = 0.5,
qvalueCutoff = 0.5,
readable = TRUE)
Error in data.frame(..., check.names = FALSE) : 行名里有缺失值

but, running "BP", "MF",or "CC" separately, they all success.

R 4.4.0
clusterprofiler 4.12.2

[guidohooiveld]

It is working in my hands with the example code. See below.

I noticed you are indeed using the latest version of clusterProfiler (i.e. 4.12.2), but maybe your Bioconductor installation is not yet up-to-date. Note the version of the GO.db library (3.19.1).

Therefore I recommend to update your complete Bioconductor installation (to version 3.19); in a fresh R session run: BiocManager::install(version = "3.19")

> library(clusterProfiler)
> library(org.Hs.eg.db)
> 
> data(geneList, package="DOSE")
> gene <- names(geneList)[abs(geneList) > 2]
> 
> 
> ego <- enrichGO(gene          = gene,
+                 universe      = names(geneList),
+                 OrgDb         = org.Hs.eg.db,
+                 ont           = "ALL",
+                 pAdjustMethod = "BH",
+                 pvalueCutoff  = 0.01,
+                 qvalueCutoff  = 0.05,
+                 readable      = TRUE)
> 
> ego
#
# over-representation test
#
#...@organism    Homo sapiens 
#...@ontology    GOALL 
#...@keytype     ENTREZID 
#...@gene        chr [1:207] "4312" "8318" "10874" "55143" "55388" "991" "6280" "2305" ...
#...pvalues adjusted by 'BH' with cutoff <0.01 
#...152 enriched terms found
'data.frame':   152 obs. of  10 variables:
 $ ONTOLOGY   : chr  "BP" "BP" "BP" "BP" ...
 $ ID         : chr  "GO:0098813" "GO:0000070" "GO:0000819" "GO:0140014" ...
 $ Description: chr  "nuclear chromosome segregation" "mitotic sister chromatid segregation" "sister chromatid segregation" "mitotic nuclear division" ...
 $ GeneRatio  : chr  "34/197" "28/197" "30/197" "32/197" ...
 $ BgRatio    : chr  "238/11586" "152/11586" "185/11586" "224/11586" ...
 $ pvalue     : num  3.73e-22 1.91e-21 3.02e-21 7.01e-21 7.30e-21 ...
 $ p.adjust   : num  1.12e-18 2.88e-18 3.03e-18 4.40e-18 4.40e-18 ...
 $ qvalue     : num  1.03e-18 2.65e-18 2.79e-18 4.05e-18 4.05e-18 ...
 $ geneID     : chr  "CDCA8/CDC20/KIF23/CENPE/MYBL2/CCNB2/NDC80/TOP2A/NCAPH/ASPM/DLGAP5/UBE2C/SKA1/NUSAP1/TPX2/TACC3/NEK2/CDK1/MAD2L1"| __truncated__ "CDCA8/CDC20/KIF23/CENPE/MYBL2/NDC80/NCAPH/DLGAP5/UBE2C/SKA1/NUSAP1/TPX2/NEK2/CDK1/MAD2L1/KIF18A/CDT1/BIRC5/KIF1"| __truncated__ "CDCA8/CDC20/KIF23/CENPE/MYBL2/NDC80/TOP2A/NCAPH/DLGAP5/UBE2C/SKA1/NUSAP1/TPX2/TACC3/NEK2/CDK1/MAD2L1/KIF18A/CDT"| __truncated__ "CDCA8/CDC20/KIF23/CENPE/MYBL2/NDC80/NCAPH/DLGAP5/UBE2C/SKA1/NUSAP1/TPX2/NEK2/UBE2S/CDK1/MAD2L1/KIF18A/CDT1/BIRC"| __truncated__ ...
 $ Count      : int  34 28 30 32 37 37 38 23 39 37 ...
#...Citation
 T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu.
 clusterProfiler 4.0: A universal enrichment tool for interpreting omics data.
 The Innovation. 2021, 2(3):100141 

> head(as.data.frame(ego))
           ONTOLOGY         ID                          Description GeneRatio
GO:0098813       BP GO:0098813       nuclear chromosome segregation    34/197
GO:0000070       BP GO:0000070 mitotic sister chromatid segregation    28/197
GO:0000819       BP GO:0000819         sister chromatid segregation    30/197
GO:0140014       BP GO:0140014             mitotic nuclear division    32/197
GO:0007059       BP GO:0007059               chromosome segregation    37/197
GO:0000280       BP GO:0000280                     nuclear division    37/197
             BgRatio       pvalue     p.adjust       qvalue
GO:0098813 238/11586 3.730986e-22 1.124892e-18 1.034858e-18
GO:0000070 152/11586 1.909540e-21 2.878631e-18 2.648230e-18
GO:0000819 185/11586 3.017475e-21 3.032563e-18 2.789841e-18
GO:0140014 224/11586 7.008600e-21 4.403280e-18 4.050849e-18
GO:0007059 319/11586 7.302289e-21 4.403280e-18 4.050849e-18
GO:0000280 327/11586 1.726930e-20 8.677821e-18 7.983262e-18
                                                                                                                                                                                                                                 geneID
GO:0098813                     CDCA8/CDC20/KIF23/CENPE/MYBL2/CCNB2/NDC80/TOP2A/NCAPH/ASPM/DLGAP5/UBE2C/SKA1/NUSAP1/TPX2/TACC3/NEK2/CDK1/MAD2L1/KIF18A/CDT1/BIRC5/KIF11/TTK/NCAPG/AURKB/TRIP13/PRC1/KIFC1/KIF18B/AURKA/CCNB1/KIF4A/PTTG1
GO:0000070                                                        CDCA8/CDC20/KIF23/CENPE/MYBL2/NDC80/NCAPH/DLGAP5/UBE2C/SKA1/NUSAP1/TPX2/NEK2/CDK1/MAD2L1/KIF18A/CDT1/BIRC5/KIF11/TTK/NCAPG/AURKB/TRIP13/PRC1/KIFC1/KIF18B/CCNB1/KIF4A
GO:0000819                                            CDCA8/CDC20/KIF23/CENPE/MYBL2/NDC80/TOP2A/NCAPH/DLGAP5/UBE2C/SKA1/NUSAP1/TPX2/TACC3/NEK2/CDK1/MAD2L1/KIF18A/CDT1/BIRC5/KIF11/TTK/NCAPG/AURKB/TRIP13/PRC1/KIFC1/KIF18B/CCNB1/KIF4A
GO:0140014                                 CDCA8/CDC20/KIF23/CENPE/MYBL2/NDC80/NCAPH/DLGAP5/UBE2C/SKA1/NUSAP1/TPX2/NEK2/UBE2S/CDK1/MAD2L1/KIF18A/CDT1/BIRC5/KIF11/TTK/NCAPG/AURKB/CHEK1/TRIP13/PRC1/KIFC1/KIF18B/AURKA/CCNB1/KIF4A/BMP4
GO:0007059   CDCA8/CDC20/KIF23/CENPE/MYBL2/CCNB2/NDC80/TOP2A/NCAPH/ASPM/DLGAP5/UBE2C/HJURP/SKA1/NUSAP1/TPX2/TACC3/NEK2/CENPM/CENPN/CDK1/MAD2L1/KIF18A/CDT1/BIRC5/KIF11/TTK/NCAPG/AURKB/TRIP13/PRC1/KIFC1/KIF18B/AURKA/CCNB1/KIF4A/PTTG1
GO:0000280 CDCA8/CDC20/KIF23/CENPE/MYBL2/CCNB2/NDC80/TOP2A/NCAPH/ASPM/DLGAP5/UBE2C/SKA1/NUSAP1/TPX2/NEK2/RAD51AP1/UBE2S/CDK1/MAD2L1/KIF18A/CDT1/BIRC5/KIF11/TTK/NCAPG/AURKB/CHEK1/TRIP13/PRC1/KIFC1/KIF18B/AURKA/CCNB1/KIF4A/PTTG1/BMP4
           Count
GO:0098813    34
GO:0000070    28
GO:0000819    30
GO:0140014    32
GO:0007059    37
GO:0000280    37
> 
> 
> packageVersion("clusterProfiler")
[1] ‘4.12.2’
> packageVersion("GO.db")
[1] ‘3.19.1’
> 
>