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

[sguttr]

I am currently trying to split my Seurat object into samples in order to follow the Integration vignette. My Seurat object is currently already split into days:

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.Day 3, counts.Day 4, counts.Day 5, counts.Day 6, counts.Day 7, data.Day 3, data.Day 4, data.Day 5, data.Day 6, data.Day 7, scale.data
2 dimensional reductions calculated: pca, umap

I tried JoinLayers to create just three layers (counts, data and scale.data) and then converted the object back into a Seurat object because JoinLayers created an Assay5 file. However, I keep getting errors when using the split function.

I am following this code:

obj[["RNA"]] <- split(obj[["RNA"]], f = obj$Method)

But I keep getting this error code:

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

If anyone could explain why this is happening and how I can rectify it, that would help. Thanks :)

[samuel-marsh]

Hi,

Can you please post the full code that you are running and the output of sessionInfo()?

Thanks,
Sam