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YuLab-SMU / biomedical-knowledge-mining-book

:books: Biomedical knowledge mining using GOSemSim and clusterProfiler
https://yulab-smu.top/biomedical-knowledge-mining-book/
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please help me #5

Open adistman opened 3 years ago

adistman commented 3 years ago

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 commented 3 years ago

can you provide sample data to reproduce this issue?

adistman commented 3 years ago

could you tell me what is wrong with this program