clusterProfiler
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Error in get("GO2ONT", envir = GO_DATA) : object 'GO2ONT' not found
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,
Please provide repeatable code with the data.
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
The code works well with me, did you use the latest version of clusterProfiler
?
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
Please try the Github version. If you still have this error, please send the data and the complete code to my email: [email protected].
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’
It is important to provide data to reproduce this error, because many errors have nothing to do with the code.
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
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
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!!!