Compatibility issues of DoubletFinder 2.0.4 with Seurat V4

[zhongguozhiwang]

Hello, may I ask if the new version of DoubletFinder can not be used in Seurat V4? I have an error when using it. Is there a good solution if I do not update Seurat? Thank you! `

packageVersion('Seurat') [1] ‘4.4.0’ packageVersion('DoubletFinder') [1] ‘2.0.4’

all.list <- lapply(X = all.list, FUN = function(x) { sweep.res.list <- paramSweep(x, PCs = 1:20, sct = FALSE) sweep.stats <- summarizeSweep(sweep.res.list, GT = FALSE) bcmvn <- find.pK(sweep.stats) pK <- bcmvn$pK[which.max(bcmvn$BCmetric)] %>% as.character() %>% as.numeric() DoubletRate <- ncol(x)/100000.06 homotypic.prop <- modelHomotypic(x$seurat_clusters) nExp_poi <- round(DoubletRatenrow([email protected])) nExp_poi.adj <- round(nExp_poi*(1-homotypic.prop)) x <- doubletFinder(x, PCs = 1:20, pN = 0.25, pK = pK, nExp = nExp_poi.adj, reuse.pANN = FALSE, sct = FALSE) })

Error in seu@assays$RNA$counts : $ operator not defined for this S4 class `

[Drizzle63]

I find this, you can use it try to solve this problem. remotes::install_github('lzmcboy/DoubletFinder_204_fix') I have the same version of Seurat and DoubletFinder with you,but I find that : Error in [email protected] : no applicable method for @ applied to an object of class "list" so I want to know if you would have this problem too