How do I resolve an integration error in Seurat?
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Entering edit mode
5 weeks ago
pcitrano3 • 0

I am new to Seurat, and am trying to run an integrated analysis of two different single-nuclei RNAseq datasets. I have been following the Seurat tutorial on integrated analysis (https://satijalab.org/seurat/articles/integration_introduction.html) to guide me, but when I ran the last line of code, I got an error.

# Loading required libraries
library(Seurat)
library(cowplot)
library(patchwork)

# Set up the Seurat Object
vgat.data <- Read10X(data.dir = "~/Desktop/VGAT Viral Data 1/")
vglut.data <- Read10X(data.dir = "~/Desktop/VGLUT3 Viral/")

# Initialize the Seurat object with the raw (non-normalized data)
vgat <- CreateSeuratObject(counts = vgat.data, project = "VGAT/VGLUT Integration", min.cells = 3, min.features = 200)
vglut <- CreateSeuratObject(counts = vglut.data, project = "VGAT/VGLUT Integration", min.cells = 3, min.features = 200)

# Merging the datasets
vgat <- AddMetaData(vgat, metadata = "VGAT", col.name = "Cell")
vglut <- AddMetaData(vglut, metadata = "VGLUT", col.name = "Cell")
merged <- merge(vgat, y = vglut, add.cell.ids = c("VGAT", "VGLUT"), project = "VGAT/VGLUT Integration")

# Split the dataset into a list of two seurat objects (vgat and vglut)
merged.list <- SplitObject(merged, split.by = "Cell")

# Normalize and Identify variable features for each dataset independently
merged.list <lapply(X = merged.list, FUN = function(x) {
  x <- NormalizeData(x)
  x <- FindVariableFeatures(x, selection.method = "vst", nFeatures = 2000)
})

After running the last line of code, I get the following error: Error in merged.list < lapply(X = merged.list, FUN = function(x) { : comparison of these types is not implemented

I was wondering if anyone is familiar with Seurat and knows how I can troubleshoot this error. Any help would be greatly appreciated.

R Seurat • 152 views
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Entering edit mode

You are missing "-" sign in the assignment operator.

merged.list <- lapply(X = merged.list, FUN = function(x) {
  x <- NormalizeData(x)
  x <- FindVariableFeatures(x, selection.method = "vst", nFeatures = 2000)
})
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