Error in match.arg(arg = value, choices = Assays(object = object)) : 'arg' should be one of “RNA”, “SCT”

[MonkeySylvia]

Hi,

I want to map my data to a publicly available dataset to identify cell clusters, so I followed the tutorial of "Multimodal reference mapping". Because the dataset has several timepoints, it has multiple SCT points after normalization. I've tried to integrate the layers, but it still gave me errors. ref <- SCTransform(ref, verbose = FALSE) ref <- IntegrateLayers(object = ref, method = CCAIntegration, normalization.method = "SCT",orig.reduction = "pca", new.reduction = "integrated.cca", verbose = F)

> ref An object of class Seurat 45909 features across 16535 samples within 2 assays Active assay: SCT (16457 features, 3000 variable features) 3 layers present: counts, data, scale.data 1 other assay present: RNA 4 dimensional reductions calculated: pca, umap, integrated.cca

pbmc_q <- SCTransform(pbmc, verbose = FALSE) > pbmc_q An object of class Seurat 43755 features across 39642 samples within 2 assays Active assay: SCT (21074 features, 3000 variable features) 3 layers present: counts, data, scale.data 1 other assay present: RNA 2 dimensional reductions calculated: pca, umap

This is where I got errors anchors <- FindTransferAnchors( reference = ref, query = pbmc_q, normalization.method = "SCT", reference.reduction = "pca", reference.assay = "integrated.cca", dims = 1:50 )

The error Error in match.arg(arg = value, choices = Assays(object = object)) : 'arg' should be one of “RNA”, “SCT”

Thank you for any suggestions!

Best, Sylvia

[SJTU-wyk]

me too! I encountered the same mistake when running runProjectils