How should I solve the error: comparison (3) is possible only for atomic and list types
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
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