Hello, author,
When I was using scanorama for single-cell data integration in R, I encountered difficulties but have not been able to solve them, so I would like to seek help from your team. The specific code and errors are as follows:
Code
library(reticulate)
library(tidyverse)
library(Seurat)
library(Matrix)
Error
Found 13402 genes among all datasets
Error in py_call_impl(callable, call_args$unnamed, call_args$named) :
IndexError: index (14510) out of range
Run reticulate::py_last_error() for details. @
Hello, author, When I was using scanorama for single-cell data integration in R, I encountered difficulties but have not been able to solve them, so I would like to seek help from your team. The specific code and errors are as follows: Code library(reticulate) library(tidyverse) library(Seurat) library(Matrix)
Specify Python virtual environment
use_python("/Software/PythonENV/xteam.py3.8/bin/python", required = TRUE)
Import necessary Python packages
scanorama <- import("scanorama")
Generate random matrix
seurat_obj1 <- readRDS("/IData/DataCenter/ColorectalCancer/Chen_Cell_2021_CRC/scRNAseq.processed.rds") seurat_obj2 <- readRDS("/IData/DataCenter/ColorectalCancer/Giguelay_Theranostics_2022/scRNAseq.processed.ok.rds")
Extract sparse count matrix
seurat_obj1_counts <- seurat_obj1@assays $ RNA@counts seurat_obj2_counts <- seurat_obj2@assays $ RNA@counts X1 <- as.matrix(seurat_obj1_counts) genes1 <- rownames(seurat_obj1_counts) genes1[1:5] X2 <- as.matrix(seurat_obj2_counts) genes2 <- rownames(seurat_obj2_counts)
Put the data into the list
datasets <- list(X1, X2) genes_list <- list(genes1, genes2)
Use Scanorama for data integration
integrated_result <- scanorama$integrate(datasets, genes_list)
Error Found 13402 genes among all datasets Error in py_call_impl(callable, call_args$unnamed, call_args$named) : IndexError: index (14510) out of range Run
reticulate::py_last_error()for details. @