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Update Seurat object pbmcsca used in Integration tutorial #86

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rbutleriii opened this issue Apr 24, 2024 · 0 comments
Open

Update Seurat object pbmcsca used in Integration tutorial #86

rbutleriii opened this issue Apr 24, 2024 · 0 comments

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@rbutleriii
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Running the tutorial for Integration in Seurat v5, and the pbmcsca object needs updating, b/c its throwing an error

# after Installing via InstallData(), still needs some work.
> obj <- LoadData("pbmcsca")
> obj
Error: Please run UpdateSeuratObject on your object
> obj <- UpdateSeuratObject(obj)
Validating object structure
Updating object slots
Ensuring keys are in the proper structure
Warning: Assay RNA changing from Assay to Assay
Ensuring keys are in the proper structure
Ensuring feature names don't have underscores or pipes
Updating slots in RNA
Validating object structure for Assay 'RNA'
Object representation is consistent with the most current Seurat version

Similarly, a lot of warnings and errors as the tutorial continues:

> obj <- RunAzimuth(obj, reference = "pbmcref")
An AzimuthData object - reference version: 1.0.0
Contains 3 meta.data field(s) to transfer.Error in validObject(object = object) :
  invalid class "Assay5" object: Layers must be two-dimensional objects
> obj
An object of class Seurat
33694 features across 10434 samples within 1 assay
Active assay: RNA (33694 features, 0 variable features)
 2 layers present: counts, data
> obj[["RNA"]] <- split(obj[["RNA"]], f = obj$Method)
Warning: Assay RNA changing from Assay to Assay5
Warning message:
Input is a v3 assay and `split()` only works for v5 assays; convertingto a v5 assay
> obj
An object of class Seurat
33694 features across 10434 samples within 1 assay
Active assay: RNA (33694 features, 0 variable features)
 18 layers present: counts.Smart-seq2, counts.CEL-Seq2, counts.10x_Chromium_v2_A, counts.10x_Chromium_v2_B, counts.10x_Chromium_v3, counts.Drop-seq, counts.Seq-Well, counts.inDrops, counts.10x_Chromium_v2, data.Smart-seq2, data.CEL-Seq2, data.10x_Chromium_v2_A, data.10x_Chromium_v2_B, data.10x_Chromium_v3, data.Drop-seq, data.Seq-Well, data.inDrops, data.10x_Chromium_v2
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