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Error in methods :: slot(object = object, name = "layers") [[layers]][features, : incorrect number of dimensions, a problem Seurat V5 #9577

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Vincent8484 opened this issue Dec 26, 2024 · 1 comment

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@Vincent8484
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Vincent8484 commented Dec 26, 2024

Hi everybody, i'm just want to use NormalizeData in Seurat, I checked error like: MergeGSE254918_Healthy[["RNA"]]

Assay (v5) data with 26202 features for 3 cells
First 10 features:
A1BG, A1BG-AS1, A1CF, A2M, A2M-AS1, A2ML1, A2MP1, A3GALT2, A4GALT, A4GNT
Layers:
counts.3, counts.4
names(MergeGSE254918_Healthy@assays)
"RNA"

code:
MergeGSE254918_Healthy <- NormalizeData (MergeGSE254918_Healthy, normalization.method = "LogNormalize", scale.factor = 1000, assay = "RNA")

Error:

Error in methods::slot(object = object, name = "layers")[[layer]][features, :
incorrect number of dimensions

help me, how to solve this problem hix hix

@Vincent8484 Vincent8484 changed the title Error in methods :: slot(object = object, name = "layers") [[layers]][features, : Error in methods :: slot(object = object, name = "layers") [[layers]][features, : incorrect number of dimensions Dec 26, 2024
@Vincent8484
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i'm trying to NormalizeData as follow:
sc_ob <- NormalizeData(sc_ob, normalization.method = "LogNormalize", scale.factor = 1000, assay = "RNA"

Error:
Error in methods :: slot(object = object, name = "layers") [[layers]][features, :
incorrect number of dimensions
pls help mee

@Vincent8484 Vincent8484 changed the title Error in methods :: slot(object = object, name = "layers") [[layers]][features, : incorrect number of dimensions Error in methods :: slot(object = object, name = "layers") [[layers]][features, : incorrect number of dimensions, Dec 27, 2024
@Vincent8484 Vincent8484 changed the title Error in methods :: slot(object = object, name = "layers") [[layers]][features, : incorrect number of dimensions, Error in methods :: slot(object = object, name = "layers") [[layers]][features, : incorrect number of dimensions, a problem Seurat V5 Dec 27, 2024
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