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Hi,
I am trying to reproduce the example code provided below and i get an error
> data(geneList, package = "DOSE")
> de <- names(geneList)[1:100]
> yy <- enrichGO(de, 'org.Hs.eg.db', ont="BP", pvalueCutoff=0.01)
> head(yy)
ID Description GeneRatio BgRatio RichFactor FoldEnrichment zScore pvalue
GO:0007059 GO:0007059 chromosome segregation 34/99 431/18805 0.07888631 14.98441 21.36650 4.744689e-31
GO:0098813 GO:0098813 nuclear chromosome segregation 31/99 322/18805 0.09627329 18.28706 22.76225 6.561567e-31
GO:0000819 GO:0000819 sister chromatid segregation 28/99 234/18805 0.11965812 22.72900 24.33225 1.457950e-30
GO:0000070 GO:0000070 mitotic sister chromatid segregation 26/99 193/18805 0.13471503 25.58905 24.97906 9.463712e-30
GO:0140014 GO:0140014 mitotic nuclear division 29/99 282/18805 0.10283688 19.53381 22.81319 1.026099e-29
GO:0000280 GO:0000280 nuclear division 33/99 448/18805 0.07366071 13.99182 20.24698 3.996836e-29
p.adjust qvalue
GO:0007059 5.367362e-28 4.306460e-28
GO:0098813 5.367362e-28 4.306460e-28
GO:0000819 7.950689e-28 6.379172e-28
GO:0000070 3.357397e-27 2.693781e-27
GO:0140014 3.357397e-27 2.693781e-27
GO:0000280 1.089804e-26 8.743954e-27
geneID
GO:0007059 55143/991/9493/1062/4605/9133/10403/7153/23397/259266/9787/11065/55355/220134/51203/22974/10460/4751/79019/55839/983/4085/81930/81620/332/3832/7272/64151/9212/9319/9055/3833/146909/6790
GO:0098813 55143/991/9493/1062/4605/9133/10403/7153/23397/259266/9787/11065/220134/51203/22974/10460/4751/983/4085/81930/81620/332/3832/7272/64151/9212/9319/9055/3833/146909/6790
GO:0000819 55143/991/9493/1062/4605/10403/7153/23397/9787/11065/220134/51203/22974/10460/4751/983/4085/81930/81620/332/3832/7272/64151/9212/9319/9055/3833/146909
GO:0000070 55143/991/9493/1062/4605/10403/23397/9787/11065/220134/51203/22974/4751/983/4085/81930/81620/332/3832/7272/64151/9212/9319/9055/3833/146909
GO:0140014 55143/991/9493/1062/4605/10403/23397/9787/11065/220134/51203/22974/4751/27338/983/4085/81930/81620/332/3832/7272/64151/9212/1111/9319/9055/3833/146909/6790
GO:0000280 55143/991/9493/1062/4605/9133/10403/7153/23397/259266/9787/11065/220134/51203/22974/4751/10635/27338/983/4085/81930/81620/332/3832/7272/64151/9212/1111/9319/9055/3833/146909/6790
Count
GO:0007059 34
GO:0098813 31
GO:0000819 28
GO:0000070 26
GO:0140014 29
GO:0000280 33
This is the error, the object contains the ontology so dont know the problem ?
> goplot(yy)
Error in goplot.enrichResult(x, showCategory = showCategory, color = color, :
Ontology should be one of 'MF', 'CC' or 'BP'
> yy@ontology
[1] "BP"
Subset of the returned yy object:
> str(yy)
Formal class 'enrichResult' [package "DOSE"] with 15 slots
..@ result :'data.frame': 1636 obs. of 12 variables:
.. ..$ ID : chr [1:1636] "GO:0007059" "GO:0098813" "GO:0000819" "GO:0000070" ...
.. ..$ Description : chr [1:1636] "chromosome segregation" "nuclear chromosome segregation" "sister chromatid segregation" "mitotic sister chromatid segregation" ...
.. ..$ GeneRatio : chr [1:1636] "34/99" "31/99" "28/99" "26/99" ...
.. ..$ BgRatio : chr [1:1636] "431/18805" "322/18805" "234/18805" "193/18805" ...
.. ..$ RichFactor : num [1:1636] 0.0789 0.0963 0.1197 0.1347 0.1028 ...
.. ..$ FoldEnrichment: num [1:1636] 15 18.3 22.7 25.6 19.5 ...
.. ..$ zScore : num [1:1636] 21.4 22.8 24.3 25 22.8 ...
.. ..$ pvalue : num [1:1636] 4.74e-31 6.56e-31 1.46e-30 9.46e-30 1.03e-29 ...
.. ..$ p.adjust : num [1:1636] 5.37e-28 5.37e-28 7.95e-28 3.36e-27 3.36e-27 ...
.. ..$ qvalue : num [1:1636] 4.31e-28 4.31e-28 6.38e-28 2.69e-27 2.69e-27 ...
.. ..$ geneID : chr [1:1636] "55143/991/9493/1062/4605/9133/10403/7153/23397/259266/9787/11065/55355/220134/51203/22974/10460/4751/79019/5583"| __truncated__ "55143/991/9493/1062/4605/9133/10403/7153/23397/259266/9787/11065/220134/51203/22974/10460/4751/983/4085/81930/8"| __truncated__ "55143/991/9493/1062/4605/10403/7153/23397/9787/11065/220134/51203/22974/10460/4751/983/4085/81930/81620/332/383"| __truncated__ "55143/991/9493/1062/4605/10403/23397/9787/11065/220134/51203/22974/4751/983/4085/81930/81620/332/3832/7272/6415"| __truncated__ ...
.. ..$ Count : int [1:1636] 34 31 28 26 29 33 33 21 20 17 ...
..@ pvalueCutoff : num 0.01
..@ pAdjustMethod: chr "BH"
..@ qvalueCutoff : num 0.2
..@ organism : chr "Homo sapiens"
..@ ontology : chr "BP"
..@ gene : chr [1:100] "4312" "8318" "10874" "55143" ...
..@ keytype : chr "ENTREZID"
..@ universe : chr [1:18805] "142" "291" "1763" "1890" ...
..@ gene2Symbol : chr(0)
..@ geneSets :List of 2248
.. ..$ GO:0000018: chr [1:142] "25" "60" "86" "142" ...
.. ..$ GO:0000022: chr [1:12] "332" "3619" "4926" "6795" ...
.. ..$ GO:0000070: chr [1:193] "324" "332" "387" "472" ...
...
.. .. [list output truncated]
..@ readable : logi FALSE
..@ termsim : num[0 , 0 ]
..@ method : chr(0)
..@ dr : list()
>
Running the packages below for clusterProfiler and R
packageVersion("clusterProfiler")
[1] ‘4.16.0’
R.version
_
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 4
minor 5.0
year 2025
month 04
day 11
svn rev 88135
language R
version.string R version 4.5.0 (2025-04-11)
nickname How About a Twenty-Six
Any idea of what is wrong ???
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