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irGSEA.integrate #33
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首先,检查一下是否有
如果存在,随机挑一个Assay检查一下这些基因集是否真的在这些细胞类型中存在差异;
以上方法都失败的话,我们要先用示例数据测试一下irGSEA流程是否顺畅。
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好的,非常感谢您,我会尽快尝试。有问题再跟您交流,辛苦了!
------------------ Original ------------------
From: ***@***.***>;
Date: Sat, Mar 2, 2024 11:50 PM
To: ***@***.***>;
Cc: ***@***.***>; ***@***.***>;
Subject: Re: [chuiqin/irGSEA] irGSEA.integrate (Issue #33)
首先,检查一下是否有celltype这一列存在,以及随机挑选一个Assay验证一下是否存在,可以这样操作:
unique(Neutrophi_rename.final2$celltype) ***@***.***[1:2,1:2]
如果存在,随机挑一个Assay检查一下这些基因集是否真的在这些细胞类型中存在差异;
Idents(Neutrophi_rename.final2) <- Neutrophi_rename.final2$celltype a <- Seurat::FindAllMarkers(object = Neutrophi_rename.final2, assay = "AUCell", slot = "scale.data", test.use = "wilcox", min.pct = -Inf, logfc.threshold = 0, min.cells.group = 0, min.diff.pct = -Inf, verbose = F, min.cells.feature = 0)
以上方法都失败的话,我们要先用示例数据测试一下irGSEA流程是否顺畅。
如果示例数据跑irGSEA流程不顺畅,说明安装存在问题:
# load PBMC dataset by R package SeuratData library(Seurat) library(SeuratData) # download 3k PBMCs from 10X Genomics InstallData("pbmc3k") data("pbmc3k.final") pbmc3k.final <- SeuratObject::UpdateSeuratObject(pbmc3k.final) # Seurat object pbmc3k.final <- irGSEA.score(object = pbmc3k.final, assay = "RNA", slot = "data", msigdb = T, species = "Homo sapiens", category = "H", geneid = "symbol", method = c("AUCell", "UCell", "singscore", "ssgsea"), kcdf = 'Gaussian') # Integrated analysis result.dge <- irGSEA.integrate(object = pbmc3k.final, group.by = "seurat_annotations", metadata = NULL, col.name = NULL, method = c("AUCell","UCell","singscore","ssgsea"))
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用的seurat.V5对象,进行时出现报错,请问该如何解决呢?麻烦了
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