Error with RunCellQC with seuratV5 object

[Kiliankleemann]

I get the following error:
Error in RunCellQC(srt = dataset) :
The db_rate is equal to or greater than 1!

My seurat object:
Assay (v5) data with 20167 features for 109037 cells
Top 10 variable features:
S100a9, S100a8, Plp1, Ngp, Retnlg, Camp, Lcn2, Gzma, Ltf, Ccl5
Layers:
data, counts, scale.data

[YongjieWangSarcoma]

You can add a new assay without layer.

提取现有RNA assay中的counts数据

counts_data <- LayerData(object = obj, assay = "RNA", layer = "counts")

创建一个新的Assay对象

new_assay <- CreateAssayObject(counts = counts_data)

将新的Assay对象添加到Seurat对象中并命名为RNA1

obj[["RNA1"]] <- new_assay

检查Seurat对象中的assays

print(Assays(obj))

obj <- RunCellQC(srt = obj,assay = "RNA1")

It will work.

[Kiliankleemann]

Xie Xie!

[mengxu98]

目前SCP还不支持seurat v5对象，可以参考#236对Seurat包进行降级。