Error in get("GO2ONT", envir = GO_DATA) : object 'GO2ONT' not found

[jarpin90]

Thanks professor.

I have been using clusterProfiler for 3 months, and I have never experienced this error before. It only happens when aiming at doing a GSEA from an ENSEMBL gene list. My list is ordered and preset and works well with other functions in the package. I am using a pvalueCutoff = 0.01, and 1000 permutations.

Could you please help me out?
I need this with urgency for a presentation next week, and because of a system crash (while running the package, I've lost my progress in the working environment)

here is my code:

gse.CADi <- gseGO(geneList = gene_list_CADi, ont = "ALL", keyType = "ENSEMBL", minGSSize = 50, maxGSSize = 800, pAdjustMethod = "BH", pvalueCutoff = 0.01, verbose = TRUE, nPermSimple=10000, OrgDb = organism)

Thank you again and all the best,

[huerqiang]

Please provide repeatable code with the data.

[jarpin90]

Hi Erquiang, This is the code:

`gseGO(geneList = data
                 ont = "ALL",
                 keyType = "ENSEMBL", 
                 minGSSize = 50, 
                 maxGSSize = 800, 
                 pAdjustMethod = "BH",
                 pvalueCutoff = 0.05,
                 verbose = TRUE, 
                 nPermSimple=1000,
                 OrgDb = organism)`

"data"= geneList, ordered in descending logFC with Enseml IDs, all the rest are the settings included in the gseGO function. Thanks

[huerqiang]

The code works well with me, did you use the latest version of clusterProfiler?

[jarpin90]

Yes, I am using the version 4.4.4. Should I be using an older version instead? Thank you > packageVersion('clusterProfiler') [1] 4.4.4

[huerqiang]

Please try the Github version. If you still have this error, please send the data and the complete code to my email: [email protected].

[DittmanC]

same error here Error in get("GO2ONT", envir = GO_DATA) : object 'GO2ONT' not found

packageVersion('org.Hs.eg.db') [1] ‘3.15.0’ packageVersion('clusterProfiler') [1] ‘4.4.4’

[huerqiang]

It is important to provide data to reproduce this error, because many errors have nothing to do with the code.

[michaelian93]

Hi all.

Has this issue been solved yet? I keep getting this exact error. Please note that I am relatively new to R/R Studio and this is my first time trying out clusterProfiler, so apologies in advance.

I used a dataframe containing UNIPROT in the first column and logFC in the second, prepared a genelist and sorted it. I'm unsure on how I should preferably provide sample data to reproduce the error, but I also got this same error whilst working with drosophila sample date from "https://learn.gencore.bio.nyu.edu/wp-content/uploads/2019/10/drosphila_example_de.csv" (and adjusted the organism accordingly). I really hope someone can help. Thanks in advance.

My code is as follows:

organism = "org.Hs.eg.db" BiocManager::install("org.Hs.eg.db", character.only = TRUE) library(organism, character.only=TRUE)

gse <- gseGO(geneList=gene_list, ont ="ALL", OrgDb= organism, keyType = "UNIPROT", minGSSize = 3, maxGSSize = 800, pvalueCutoff = 0.05, verbose = TRUE, pAdjustMethod = "none")

UPDATE: i have tried with both the Bioconductor and the GitHub development package, but the same error keeps cropping up

[michaelian93]

Hi all, For me the issue was solved once i switched ont="ALL" to only one component, for instance ont="BP" Hope that's helpful for anyone

[zddda58]

大家好，对我来说，一旦我将 ont=“ALL” 切换到一个组件，问题就解决了，例如 ont=“BP” 希望这对任何人都有帮助

Hello, I got the same error. I don't know, but your approach really worked. Thank you so much!!!