Seurat V5 return unscaled data

[kathdong]

Hi all, I am using Seurat V5 and V4 to analyze some scRNA datasets. The result I get from V5 integrateLayer integration method is similar to the result I get after changing DefaultAssay into "RNA" using V4 SelectIntegrationFeatures+ FindIntegrationAnchors+ IntegrateData method. Here is the code and the graph, do anyone have an idea why??

V5

V4(DefaultAssay(data) <- "integrated" )

V4(DefaultAssay(data) <- "RNA" )

V4
data.list <- list(sample1, sample2, sample3)
data.list <- lapply(X = data.list, FUN = function(x) {
x <- NormalizeData(x)
x <- FindVariableFeatures(x, selection.method = "vst", nfeatures = 2000)
})

features <- SelectIntegrationFeatures(object.list = data.list)
data.anchors <- FindIntegrationAnchors(object.list = data.list, anchor.features = features, reduction = "cca")
data.combined <- IntegrateData(anchorset = data.anchors)
DefaultAssay(data.combined) <- "integrated"
data.combined <- ScaleData(data.combined, verbose = FALSE)

data.combined <- RunPCA(data.combined)
seurat_obj_after <- runHarmony(combined,group.by.vars = "Group")
seurat_obj_after_20 <- RunUMAP(seurat_obj_after, reduction = "harmony", dims = 1:20)
seurat_obj_after_20 <- FindNeighbors(seurat_obj_after_05, reduction = "harmony", dims = 1:20)
seurat_obj_after_2009 <- FindClusters(seurat_obj_after_05, resolution = 0.9)

V5
merged_seurat <- merge(x = sample1, y = c(sample2,sample3))
dat <- NormalizeData(merged_seurat)
dat <- FindVariableFeatures(dat, selection.method = "vst", nfeatures = 2000)
dat <- ScaleData(dat, features = rownames(dat))
data.combined_PCA <- RunPCA(dat)
data.combined_integrated <- IntegrateLayers(object = data.combined_PCA, method = HarmonyIntegration,
orig.reduction = "pca", new.reduction = "harmony" ,verbose = T)
data.combined_20 <- FindNeighbors(data.combined_integrated, reduction = "harmony", dims = 1:20)
data.combined_2095 <- FindClusters(data.combined_20, resolution = 0.95)
data.combined_2095 <- RunUMAP(data.combined_2095, reduction = "harmony", dims = 1:20, reduction.name = "umap.harmony")
joined <- joinLayer(data.combined_2095)