运行JASMINE时报错停止

[1667857557]

window中运行时报错停止

> pbmc3k.final <- irGSEA.score(object = sc, assay = "RNA", 
+                              slot = "data", seeds = 123, ncores = 10,
+                              min.cells = 3, min.feature = 0,
+                              custom = F, geneset = NULL, msigdb = T, 
+                              species = "Homo sapiens", category = "C2", subcategory="CP:KEGG", geneid = "symbol",
+                              method = c("JASMINE"),
+                              aucell.MaxRank = NULL, ucell.MaxRank = NULL, 
+                              kcdf = 'Gaussian')
Validating object structure
Updating object slots
Ensuring keys are in the proper structure
Ensuring keys are in the proper structure
Ensuring feature names don't have underscores or pipes
Updating slots in RNA
Validating object structure for Assay5 ‘RNA’
Object representation is consistent with the most current Seurat version
Calculate JASMINE scores
Warning messages:
1: Layer ‘data’ is empty 
2: In BiocParallel::MulticoreParam(workers = ncores) :
  MulticoreParam() not supported on Windows, use SnowParam()

[chuiqin]

方便的话，加我微信fcq065837，我来测试一下你的数据

[chuiqin]

一个可能的猜测是，sc是一个Assay5对象，但里面的lays只有counts，没有data，因此可以尝试把irGSEA.score中的参数从'data'改成'counts'。PS：新版本的irGSEA才支持Seurat V5。