Hi! I am trying to run scType to annotate a total of 18 clusters obtained following Xenium Spatial Transcriptomics (tissue type is pituitary). I am running the script however I keep encountering the following error (code included):
Annotating via scType
Step 1: Call packages via library function
library(dplyr) library(Seurat) library(HGNChelper) library(openxlsx)
Step 2: Install scType source files
source("https://raw.githubusercontent.com/IanevskiAleksandr/sc-type/master/R/gene_sets_prepare.R") source("https://raw.githubusercontent.com/IanevskiAleksandr/sc-type/master/R/sctype_score_.R") source("https://raw.githubusercontent.com/IanevskiAleksandr/sc-type/master/R/sctype_wrapper.R")
Loading in custom markers
Read the marker file
markers <- read.xlsx("scTypeDB_short.xlsx") head(markers)
Step 3: Run scType on Seurat object
Run scType with your Seurat object and custom markers
xen <- run_sctype(xen, assay = "Xenium", scaled = TRUE, known_tissue_type = "Pituitary", custom_marker_file = "scTypeDB_short.xlsx", name = "sctype_classification")
[1] "Using Seurat v5 object" Error in (function (cond) : error in evaluating the argument 'x' in selecting a method for function 'rowSums': subscript out of bounds In addition: There were 50 or more warnings (use warnings() to see the first 50)
Would appreciate any help thanks!