How should I solve the error: comparison (3) is possible only for atomic and list types
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19 months ago
paria ▴ 90

Hi all, I'm trying to integrate my single cell dataset using reciprocal pea instead of pca in Seurat. Below is the code I run. The integration was done successfully. However, I'm getting the below error after trying to ScaleData. I couldn't find any solution for this in others posts.

#the code I applied on merged filtered dataset
split_seurat <- SplitObject(filtered_seurat, split.by = "orig.ident")
split_seurat <- lapply(X = split_seurat, FUN = function(x) {
    x <- NormalizeData(x, verbose = FALSE)
    x <- FindVariableFeatures(x, verbose = FALSE)
})

#Data integration
integ_features <- SelectIntegrationFeatures(object.list = split_seurat, nfeatures = 2000)
split_seurat <- lapply(X = split_seurat, FUN = function(x) {
    x <- ScaleData(x, features = integ_features, verbose = FALSE)
    x <- RunPCA(x, features = integ_features, npcs = 80,verbose = FALSE)
})

integ_anchors <- FindIntegrationAnchors(object.list = split_seurat, anchor.features = 1000, reference = c(2, 3, 11, 13), reduction = "rpca", dims = 1:80)
seurat_integrated <- IntegrateData(anchorset = integ_anchors, dims = 1:80)

seurat_integrated < ScaleData(seurat_integrated, verbose = FALSE)

Error in seurat_integrated < ScaleData(seurat_integrated, verbose = FALSE) : 
  comparison (3) is possible only for atomic and list types

Does anybody know why I'm getting this error and how I could solve it? I appreciate any input on this. Thanks, Paria

single ScaleData cell rpca analysis • 2.4k views
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s/</<-/

Low-effort question, low-effort answer

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1
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Referring to the line:

seurat_integrated < ScaleData(seurat_integrated, verbose = FALSE)
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