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please help me #5

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adistman opened this issue Aug 19, 2021 · 2 comments
Open

please help me #5

adistman opened this issue Aug 19, 2021 · 2 comments

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@adistman
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def <- FindMarkers(sub.1, ident.1 = 'case', ident.2 = 'control', group.by = 'group',logfc.threshold = 0,min.pct = 0.0001,min.diff.pct = -Inf)

data(geneList)

geneList <- def$avg_logFC

names(geneList) <- rownames(def)

geneList <- sort(geneList,decreasing = T)
geneset <- read.gmt("c2.all.v7.2.symbols.gmt")
egmt <- GSEA(geneList, TERM2GENE = geneset, minGSSize = 1, pvalueCutoff = 0.99,verbose = F)

when I did "egmt", the error show that
"Error in if (maxP > -minP) { : missing value where TRUE/FALSE needed
In addition: Warning message:
In preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, :
There are ties in the preranked stats (34.87% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results."

@GuangchuangYu
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can you provide sample data to reproduce this issue?

@adistman
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could you tell me what is wrong with this program

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