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YuLab-SMU / clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data
https://yulab-smu.top/biomedical-knowledge-mining-book/
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Trouble with gseKEGG on mac sonoma 14.2 #666

Open annecar opened 8 months ago

annecar commented 8 months ago

Hi I have trouble running a code that used to work perfectly before my upgrade to sonoma 14.2. I have used: gseaKEGG <- gseKEGG(geneList = foldchanges, # ordered named vector of fold changes (Entrez IDs are the associated names) organism = "hsa",

nPerm = 1000,

                 minGSSize = 100, genes
                 pvalueCutoff = 0.05, # padj cutoff value
                 verbose = FALSE)

I get this error: --> Expected input gene ID: Error in check_gene_id(geneList, geneSets) : --> No gene can be mapped....

I have updated Rstudio, (Version 2023.12.1+402 (2023.12.1+402))R (4.3.2) , clusterprofiler (4.8.3) and DOSE (3.29.2)

I would be greatfull for any help. Annecar

guidohooiveld commented 7 months ago

This has nothing to do with the upgrade, but rather that your input doesn't match with what is expected... Expected are indeed human NCBI gene ids, but somehow these are not recognized. So double-check that these are indeed human NCBI gene ids, that no leading or trailing white spaces are present in your input, and also check the ids that are returned after the error (and which you did not post here).

Also note that the current version of clusterProfiler is v4.10.0, and that of DOSE is v3.28.2. Based on the information you provided it seems that you are mixing old, release and even development versions of packages, which may cause unexpected issues. Please check this by running BiocManager::valid(), and act according to the output.