"I performed the gseGO function using clusterProfiler for all ontologies together, but I wasn't able to apply the simplify function to remove redundancy. I tried various options suggested online, but none worked. As a workaround, I ran gseGO for each ontology (BP, MF, CC) separately and then removed redundancy for each ontology using GOsim. Is it correct to combine the results from all ontologies into one file and then combining it with metadata from one ontology (e.g., the output of gseGO for BP) to create enrichment plots?" or what could be the easiest way to perfrom that #707
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Next time please properly format your post! Yet, I cannot reproduce your problem! |
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Sorry for inconvenience, Actually, I wanted to remove redundancy from the result of GSEA-GO results and then want to make an enrichemnt plot and could not a way to do that. I followed your instruction and perfrom
preparing geneSet collections...
Gene Set Enrichment Analysis#...@organism Mus musculus
Error in as.list.default(X) : Kindly tell me a way to remove redundancy from GO results and then plot it as enrichment plot |
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Again, it is working for me....! Does the exact same code from me also work for you? (copy/paste it) Note; for your specific dataset:
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Thank you very much . now it worked for me but if I applied it on Comaprecluster goGSEA, i got error message.
Result of Comparing 4 gene clusters#.. @fun gseGO #...Citation
Fehler in match.arg(ont, c("BP", "CC", "MF")) : |
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Once more, that is working for me as well!
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I am using R version 4.3.3. Initially, I unloaded the clusterProfiler package and then reinstalled it. This approach made the simplify function work for me. Unload the clusterProfiler package if it is loadedif ("package:clusterProfiler" %in% search()) { Update all outdated packagesupdate.packages(ask = FALSE) Install BiocManager if not already installedif (!requireNamespace("BiocManager", quietly = TRUE)) { Reinstall the latest version of clusterProfilerBiocManager::install("clusterProfiler", ask = FALSE) I got this code from ChatGPT However, each time before running simplify, I have to unload and reinstall clusterProfiler to get it to work again. I am not sure what is causing this issue. I re-run everything
set.seed(1)
preparing geneSet collections...
Gene Set Enrichment Analysis#...@organism Mus musculus
But it did not work for my comparecluster data and I got Fehler in match.arg(ont, c("BP", "CC", "MF")) : but now I have performed the whole analysis using the data you have mentioned data(geneList, package="DOSE")
preparing geneSet collections...
Gene Set Enrichment Analysis#...@organism Homo sapiens
same error when I perormed comaprecluster with the data
Es gab 30 Warnungen (Anzeige mit warnings())
I am extremly sorry but i did not know what is wrong. |
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Some thoughts: Since you got he error when analyzing the included human dataset, and I do not, it points to an issue with your Also, are you running it on a laptop/PC with R-studio, or on a computer cluster? Reason I am asking is because of the warning regarding the Therefore:
Also:
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I updated R from version 4.3 to 4.4.1 and updated all the packages, but the problem persists for ontology = "ALL". If I change to only one specific ontology like "BP", it works. Below, you can see the details.
R version 4.4.1 (2024-06-14 ucrt) Matrix products: default locale: time zone: Europe/Berlin attached base packages: other attached packages: loaded via a namespace (and not attached): Bioconductor version '3.19'
create a valid installation with BiocManager::install(c( more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date Warnmeldung:
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019). preparing geneSet collections...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019). preparing geneSet collections...
Gene Set Enrichment Analysis#...@organism Homo sapiens
Gene Set Enrichment Analysis#...@organism Homo sapiens
Es gab 30 Warnungen (Anzeige mit warnings())
Result of Comparing 3 gene clusters#.. @fun gseGO #...Citation
Es gab 30 Warnungen (Anzeige mit warnings())
Result of Comparing 3 gene clusters#.. @fun gseGO #...Citation
Result of Comparing 3 gene clusters#.. @fun gseGO #...Citation
Result of Comparing 3 gene clusters#.. @fun gseGO #...Citation |
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I am lost... I have the same version of Yet, I am still puzzled why you get the warnings, but I don't... Also, when I check the source code of
Below is is what I see when I check the source code in |
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I checked and get the same as you library(clusterProfiler) > selectMethod(simplify, signature="gseaResult") Method Definition: function (x, ...) { .local <- function (x, cutoff = 0.7, by = "p.adjust", select_fun = min, measure = "Wang", semData = NULL) { if (!x@setType %in% c("BP", "MF", "CC", "GOALL")) stop("simplify only applied to output from gseGO and enrichGO...") res <- as.data.frame(x) if (x@setType == "GOALL") { x@result <- simplify_ALL(res = res, cutoff = cutoff, by = by, select_fun = select_fun, measure = measure, semData = semData) } else { x@result <- simplify_internal(res = res, cutoff = cutoff, by = by, select_fun = select_fun, measure = measure, ontology = x@setType, semData = semData) } return(x) } .local(x, ...) } Signatures: x target "gseaResult" defined "gseaResult" -- > | > > |
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So:
--> I am out of suggestions... Sorry! The last thing to suggest is to use another PC or laptop... |
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Thank you very much for your support. I am now atleast able to remove redundancy from the GSEA output for a specific ontology. |
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One last remark: Again, be sure to also run the code in Another user just reported that this solved his/her problem, although that problem was not at all related to your issue... but you never know... |
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