Comments (4)
bcmvn.MM625 <- find.pK(sweep.stats.MM625)
DimPlot(object = MM625.BM, reduction = 'umap', group.by = "RNA_snn_res.0.5", label = TRUE, repel = TRUE, raster=FALSE) + NoLegend()
FeaturePlot(MM625.BM, features = "pANN_0.25_0.005_389",cols = c("yellow", "red"), reduction = 'umap', raster=FALSE) + DarkTheme()
MM625.BM <- doubletFinder_v3(MM625.BM, PCs = use.pcs, pN = 0.25, pK = mpk.MM625, nExp = nExp_poi.adj.MM625, reuse.pANN = "pANN_0.25_0.005_389", sct = FALSE)
DimPlot(MM625.BM, pt.size = 1, label = FALSE, label.size = 5, reduction = "umap", group.by = "scDblFinder.class")
DimPlot(MM625.BM,pt.size = 1,label=FALSE, label.size = 5,reduction = "umap",group.by = "DF.classifications_0.25_0.005_389")
DimPlot(MM625.BM,pt.size = 1,label=FALSE, label.size = 5,reduction = "umap",group.by = "DF.classifications_0.25_0.005_352")
MM625.singlet <- subset(x = MM625.BM, subset = DF.classifications_0.25_0.005_352 == "Singlet")
MM625.singlet
Error: Cannot find 'scDblFinder.class' in this Seurat object
why error?
from scdblfinder.
bcmvn.MM800 <- find.pK(sweep.stats.MM800)
DimPlot(object = MM800.BM, reduction = 'umap', group.by = "RNA_snn_res.0.5", label = TRUE, repel = TRUE, raster=FALSE) + NoLegend()
FeaturePlot(MM800.BM, features = "pANN_0.25_0.19_329",cols = c("yellow", "red"), reduction = 'umap', raster=FALSE) + DarkTheme()
MM800.BM <- doubletFinder_v3(MM800.BM, PCs = use.pcs, pN = 0.25, pK = mpk.MM800, nExp = nExp_poi.adj.MM800, reuse.pANN = "pANN_0.25_0.19_329", sct = FALSE)
DimPlot(MM800.BM, pt.size = 1, label = FALSE, label.size = 5, reduction = "umap", group.by = "scDblFinder.class")
DimPlot(MM800.BM,pt.size = 1,label=FALSE, label.size = 5,reduction = "umap",group.by = "DF.classifications_0.25_0.19_329")
DimPlot(MM800.BM,pt.size = 1,label=FALSE, label.size = 5,reduction = "umap",group.by = "DF.classifications_0.25_0.19_293")
MM800.singlet <- subset(x = MM800.BM, subset = DF.classifications_0.25_0.19_293 == "Singlet")
MM800.singlet
Error: None of the requested features were found: pANN_0.25_0.19_329 in slot data
In addition: Warning message:
In FetchData(object = object, vars = c(dims, "ident", features), :
The following requested variables were not found: pANN_0.25_0.19_329
MM800.BM <- doubletFinder_v3(MM800.BM, PCs = use.pcs, pN = 0.25, pK = mpk.MM800, nExp = nExp_poi.adj.MM800, reuse.pANN = "pANN_0.25_0.19_329", sct = FALSE)
Error in[.data.frame
([email protected], , reuse.pANN) :
정의하지 않은 열들이 선택되었습니다
DimPlot(MM800.BM, pt.size = 1, label = FALSE, label.size = 5, reduction = "umap", group.by = "scDblFinder.class")
Error: Cannot find 'scDblFinder.class' in this Seurat object
DimPlot(MM800.BM,pt.size = 1,label=FALSE, label.size = 5,reduction = "umap",group.by = "DF.classifications_0.25_0.19_329")
Error: Cannot find 'DF.classifications_0.25_0.19_329' in this Seurat object
DimPlot(MM800.BM,pt.size = 1,label=FALSE, label.size = 5,reduction = "umap",group.by = "DF.classifications_0.25_0.19_293")
Error: Cannot find 'DF.classifications_0.25_0.19_293' in this Seurat object
MM800.singlet <- subset(x = MM800.BM, subset = DF.classifications_0.25_0.19_293 == "Singlet")
Error in FetchData(object = object, vars = unique(x = expr.char[vars.use]), :
None of the requested variables were found:
MM800.singlet
Error: object 'MM800.singlet' not found
why error??
from scdblfinder.
bcmvn.MM482 <- find.pK(sweep.stats.MM482)
DimPlot(object = MM482.BM, reduction = 'umap', group.by = "RNA_snn_res.0.5", label = TRUE, repel = TRUE, raster=FALSE) + NoLegend()
FeaturePlot(MM482.BM, features = "scDblFinder.score", cols = c("yellow", "red"), reduction = 'umap', raster = FALSE) + DarkTheme()
FeaturePlot(MM482.BM, features = "pANN_0.25_0.005_555",cols = c("yellow", "red"), reduction = 'umap', raster=FALSE) + DarkTheme()
DimPlot(MM482.BM,pt.size = 1,label=FALSE, label.size = 5,reduction = "umap",group.by = "DF.classifications_0.25_0.005_555")
DimPlot(MM482.BM,pt.size = 1,label=FALSE, label.size = 5,reduction = "umap",group.by = "DF.classifications_0.25_0.005_483")
MM482.BM <- doubletFinder_v3(MM482.BM, PCs = use.pcs, pN = 0.25, pK = mpk.MM482, nExp = nExp_poi.adj.MM482, reuse.pANN = "pANN_0.25_0.005_555", sct = FALSE)
MM482.singlet <- subset(x = MM482.BM, subset = DF.classifications_0.25_0.005_483 == "Singlet")
MM482.singlet
FeaturePlot(MM482.BM, features = "scDblFinder.score", cols = c("yellow", "red"), reduction = 'umap', raster = FALSE) + DarkTheme()
Error: None of the requested features were found: scDblFinder.score in slot data
In addition: Warning message:
In FetchData(object = object, vars = c(dims, "ident", features), :
The following requested variables were not found: scDblFinder.score
from scdblfinder.
If you want help, you should try to make a minimum reproducible example rather than copy-pasting random chunks of mixed code and outputs. In this case the commands you run appear to be from the DoubletFinder package, so I'm not sure what you're doing here. If you want to run scDblFinder, please look at the documentation.
from scdblfinder.
Related Issues (20)
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- Filter ATAC before running scDblFinder HOT 2
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- Unreasonably high doublets rate HOT 4
- Running scDblFinder before or after normalization? HOT 2
- Error running scDblFinder HOT 3
- non-interpretable error message when providing non-integer as nfeatures argument HOT 1
- Clarify recommended nFeatures/artificialDoublets for scATACseq doublet removal in vignette HOT 2
- Doublet filtering in Parse Biosciences data HOT 6
- Unable to run scDblFinder - "as_cholmod_sparse" does not exist HOT 5
- Unable to install scDblFinder HOT 2
- Ambient RNA Removal HOT 4
- Compatibility between Seurat, matrix and scDblFinder versions HOT 4
- error in scATAC HOT 1
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from scdblfinder.