hallo,

I want to re-run the GSEA on my same data. I have previously performed the compare cluster analysis for GSEGSEA and it worked very well but now I have updated the R version to 4.4.2. here is the pathway and code with error. Kindly let me know what the issue is now

.
set.seed(1)

.....ck_TP_VL_HM<-compareCluster(geneClusters = geneList_TP_VL, fun="GSEA",TERM2GENE = hallmark_gs,

                        pAdjustMethod="fdr", 
                        seed=TRUE, by="fgsea")
Fehler in .stopf("Duplicate values in %s not allowed", universeArg) :
Duplicate values in names(stats) not allowed
Zusätzlich: Warnmeldung:
In preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, :
There are ties in the preranked stats (10.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.

The error Duplicate values in names(stats) not allowed (from fgsea that is used under the hood) shows that the input is not unique; in other words some genes are present multiple times. This often happens when gene symbols are used as identifiers.

Also cross-posted: https://github.com/YuLab-SMU/clusterProfiler/issues/754