SCTransform在seuratv4的时候没问题,升级到v5的时候不工作,出现报错
> brain <- SCTransform(rep, assay = "Spatial", verbose = TRUE)Running SCTransform on assay: SpatialRunning SC...
SCTransform在seuratv4的时候没问题,升级到v5的时候不工作,出现报错
> brain <- SCTransform(rep, assay = "Spatial", verbose = TRUE)
Running SCTransform on assay: Spatial
Running SCTransform on layer: counts
vst.flavor='v2' set. Using model with fixed slope and excluding poisson genes.
Variance stabilizing transformation of count matrix of size 20445 by 2713
Model formula is y ~ log_umi
Get Negative Binomial regression parameters per gene
Using 2000 genes, 2713 cells
Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
应该是兼容问题, 作者建议更新glmGamPoi,但是依赖也多
所以偷懒一点直接降级matrixStats就可以
remotes::install_version("matrixStats", version = "1.1.0")
在就可以执行了
