单细胞运行SCTransform；Error in .GetSeuratCompat()

Error in .GetSeuratCompat() : no".GetSeuratCompat" function. · Issue #8387 · satijalab/seurat (github.com)

https://github.com/satijalab/seurat-object/issues/165

报错及R包版本

出现报错： Error in .GetSeuratCompat() : could not find function ".GetSeuratCompat"

sce <- SCTransform(ifnb,verbose = F) #先进行SCTransform标准化
Error in .GetSeuratCompat() : could not find function ".GetSeuratCompat"

rm(list = ls())
library(SeuratData)
library(Seurat)
brain <- LoadData("stxBrain", type = "anterior1")
brain <- SCTransform(brain, assay = "Spatial", verbose = FALSE)

Error in .GetSeuratCompat() : no".GetSeuratCompat" function. -->

包：other attached packages:
[1] SeuratObject_4.1.4 Seurat_4.4.0

---

解决方法

出现问题多半是包版本和函数不匹配

解决①

请卸载并安装这些特定版本的软件包 - SeuratObject（4.1.3）、sctransform（0.3.5） 和 Seurat（4.3.0）

解决②

.GetSeuratCompat error while using SCTransform with v2 regularization

"Package": "Seurat",  "Version": "4.4.0"
"Package": "SeuratObject", "Version": "4.1.4"

GetSeuratCompat()在SeuratObject v5中引入；如果您看到的是SeuratObject v4，那么您的SeuratObject安装有问题(例如，您可能有多个安装，R变得混乱)。我建议重新启动您的会话，卸载Seurat/SeuratObject，直到您得到一个错误消息，说明软件包不存在，然后重新安装Seurat/seuratobjectremove . packages()

To reinstall Seurat/SeuratObject v5, simply install from CRAN using install.packages()

To reinstall Seurat/SeuratObject v4, use

if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}
options(repos = c("https://satijalab.r-universe.dev", getOption("repos")))
remotes::install_version("SeuratObject", "4.1.4")
remotes::install_version("Seurat", "4.4.0", upgrade = FALSE) # remotes will try to upgrade SeuratObject to v5, we need to tell it no

failed install of sctransform 0.3.5, but successful install of 0.3 satijalab/sctransform#188