RunAzimuth removes the data layer

[yeroslaviz]

I'm using Seurat 5.1 and azimuth 0.5 to analyze my data from mouse scRNA-Seq.

After loading the samples and creating the Seurat object, normalizing and identify variable feature I try to run RunAzimuth(). This works nicely, but for some reason, the data layer disappears from the Seurat object. Is this expected?

For now I'm running the Azimuth annotations using the pbmcref reference data set. I'm still looking for a good mouse reference set (specifically for myolid dendritic cells).

my workflow:

C7_G7 <- merge(C7, y =  G7, add.cell.ids = ls()[1:2], project = "C7_G7")
C7_G7 <- PercentageFeatureSet(C7_G7, pattern = "^mt-", col.name = "percent.mt")
C7_G7 <- subset(C7_G7, subset = nFeature_RNA >1000 & nFeature_RNA <6000 & nCount_RNA <1e+05 & percent.mt < 7.5 )
C7_G7 <- NormalizeData(C7_G7, normalization.method  ="LogNormalize", scale.factor = 10000)
C7_G7 <- FindVariableFeatures(C7_G7, selection.method = "mean.var.plot",
                                mean.cutoff = c(0.0125, 3),
                                dispersion.cutoff = c(0.5, Inf))
C7_G7 <- RunAzimuth(C7_G7, reference = "pbmcref")
C7_G7 <- ScaleData(C7_G7, vars.to.regress = c("nCount_RNA", "percent.mt"), verbose = TRUE) 

Here I get an error. Both when I try to run a FeaturePlot or when I try to scale the data, I'm missing the data layer.

>C7_G7
An object of class Seurat 
15247 features across 20382 samples within 4 assays 
Active assay: RNA (15152 features, 0 variable features)
 1 layer present: counts
 3 other assays present: prediction.score.celltype.l1, prediction.score.celltype.l2, prediction.score.celltype.l3
 2 dimensional reductions calculated: integrated_dr, ref.umap

This is the error:

Warning: No layers found matching search pattern providedError in `ScaleData()`:
! No layer matching pattern 'data' found. Please run NormalizeData and retry

Is the pipeline I'm going through correct? Do I need to re-do the nomrlaization step or do I need to use a different assay to plot the results of RunAzimuth?

thanks

Assa