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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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JoinLayers and split() errors #9475

Closed sguttr closed 1 week ago

sguttr commented 1 week ago

I'm currently working on a single-cell dataset and I have a merged Seurat object:

An object of class Seurat 22798 features across 1342 samples within 1 assay Active assay: RNA (22798 features, 2000 variable features) 11 layers present: counts.d3, counts.d4, counts.d5, counts.d6, counts.d7, data.d3, data.d4, data.d5, data.d6, data.d7, scale.data 2 dimensional reductions calculated: pca, umap

I'm trying to merge the count layers and data layers so I have a single count layer and a single data layer so I can integrate my data. However, when I run JoinLayers, I am left with one layer, and when I try and perform split(), I get this error:

Error in validObject(object = object) : invalid class “Assay5” object: Layers must be two-dimensional objects

How do I go about this?

sguttr commented 1 week ago

I should note I am trying to split my data differently this time rather than by day, but by sample.