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logFC error for SeuratObject from SeuratV5 #6

@PolSabt

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@PolSabt

Hello !
Nice job, the tutorial went well, but I can't run it through an classical seurat object.

When I start the following code

logfc.data <- logFC(cluster.ids=seurat_obj@meta.data$seurat_clusters ,expr.mat=seurat_obj@assays$RNA$data)
names(logfc.data)

it return

sparse->dense coercion: allocating vector of size 1.0 GiBsparse->dense coercion: allocating vector of size 1.0 GiBsparse->dense coercion: allocating vector of size 1.0 GiBsparse->dense coercion: allocating vector of size 1.0 GiBsparse->dense coercion: allocating vector of size 1.1 GiBsparse->dense coercion: allocating vector of size 1.0 GiBsparse->dense coercion: allocating vector of size 1.1 GiBsparse->dense coercion: allocating vector of size 1.1 GiBsparse->dense coercion: allocating vector of size 1.1 GiBsparse->dense coercion: allocating vector of size 1.1 GiBErreur dans apply(expr.mat[, cluster.cells[[i]]], 1, function(x) { :
dim(X) doit avoir un longueur positive

I check:

class(seurat_obj@meta.data$seurat_clusters)

[1] "factor"

head(seurat_obj@meta.data$seurat_clusters)
[1] 2 10 14 2 2 2
Levels: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

class(seurat_obj@assays$RNA$data)

[1] "dgCMatrix"
attr(,"package")
[1] "Matrix"

If you have an idea ! I appreciate

PolSabt

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