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compareCluster GSEA + universal annotation = does not work #705
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Everything points to something not being OK with your aggregated input Please note that performing GSEA with user-defined gene sets through the
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Hi,
I am working with compareCluster, trying to do a GSEA analysis using homemade annotation. To do so I decide to use Universal enrichment analysis.
I have a TERM2GENE and TERM2NAME. I am trying to run the same a GSEA (with all my genes - not only differential expressed ones). I have an error:
Error in check_gene_id(geneList, geneSets) :
--> No gene can be mapped....
Here my code (let's say input1, input2 and input3 are subsets of input):
geneList1=input1$logFC names(geneList1)=input1$Symbol geneList1=sort(geneList1, decreasing = TRUE)
geneList2=input2$logFC names(geneList2)=input2$Symbol geneList2=sort(geneList2, decreasing = TRUE)
geneList3=input3$logFC names(geneList3)=input3$Symbol geneList3=sort(geneList3, decreasing = TRUE)
geneList=c("Gut"=geneList1, "Head"=geneList2, "Abdomen"=geneList3)
gsea=compareCluster(geneList, data=input, TERM2GENE=TERM2GENE, TERM2NAME =TERM2NAME, fun="GSEA" minGSSize = 10, nPermSimple = 100000, eps=0, pvalueCutoff = 0.1, pAdjustMethod = "BH" )
This is my error:
Error in check_gene_id(geneList, geneSets) :
--> No gene can be mapped....
However, when I run the same geneLists one by one (geneList1, then geneList2 and so one) using the following code, it works perfectly (see my pictures at the end)
GSEA(geneList1, TERM2GENE=TERM2GENE, TERM2NAME =TERM2NAME, minGSSize = 10, nPermSimple = 100000, eps=0, pvalueCutoff = 0.1, pAdjustMethod = "BH" )
Some one could help me here please?
Thank you
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