Error in paramSweep_v3(scRNA_r, PCs = 1:30, sct = FALSE) : could not find function "paramSweep_v3"

[skkanlei]

When I use 'DoubletFinder'2.0.4 with seurat4.3.0, I got the Error:

sweep.res.list_keloid <- paramSweep_v3(scRNA_r, PCs = 1:30, sct = FALSE)
Error in paramSweep_v3(scRNA_r, PCs = 1:30, sct = FALSE) :
could not find function "paramSweep_v3"

I want to download DoubletFinder version 2.0.3, But I can't find method to download it.

[skkanlei]

I download the 2.0.3 by remotes::install_github('https://github.com/ekernf01/DoubletFinder', force = T)

but I still get the same error

sweep.res.list_keloid <- paramSweep_v3(scRNA_r, PCs = 1:30, sct = FALSE)
Error in paramSweep_v3(scRNA_r, PCs = 1:30, sct = FALSE) :
could not find function "paramSweep_v3"

[RunhanZhao]

You can restart the R. I did the same process as you did, and do not have this error again.

[skkanlei]

You can restart the R. I did the same process as you did, and do not have this error again.

Thank you!!! I'll have a try.

[mengm5]

Updates
(11/21/2023) Made compatible with Seurat v5 and removed '_v3' flag from relevant function names.

[SunAlan123]

I removed the '_v3' flag from the function, but there is this error again (Seurat v5). Do you know why? Thanks!

[mengm5]

I removed the '_v3' flag from the function, but there is this error again (Seurat v5). Do you know why? Thanks!

What is the error?

[SunAlan123]

I removed the '_v3' flag from the function, but there is this error again (Seurat v5). Do you know why? Thanks!

What is the error?
count not find function "paramSweep_v3"

[Yijia-Jiang]

Hi, I met the same error, could you share the script you used for seurat v5? Thank you very much!

[mengm5]

I removed the '_v3' flag from the function, but there is this error again (Seurat v5). Do you know why? Thanks!

What is the error?
count not find function "paramSweep_v3"

The key scripts I used:

sweep.res.list <- paramSweep(sceData.c, PCs = 1:30, sct = T)
sceData.c <- doubletFinder(sceData.c, PCs = 1:30, pN = 0.25, pK = pK_bcmvn, nExp = nExp_poi.adj, reuse.pANN = F, sct = T)

[mengm5]

Hi, I met the same error, could you share the script you used for seurat v5? Thank you very much!

Hi, the key scripts I used:
sweep.res.list <- paramSweep(sceData.c, PCs = 1:30, sct = T)
sceData.c <- doubletFinder(sceData.c, PCs = 1:30, pN = 0.25, pK = pK_bcmvn, nExp = nExp_poi.adj, reuse.pANN = F, sct = T)

The rest are the same as the 'Example Code' they'd given in the main page.

[Noralii]

In the specific versions of DoubletFinder 2.0.4 and Seurat 5.0.3, and after excluding 'v3', the R code sweep.res <- paramSweep(sc_tumor, PCs = doubletpc, sct = TRUE) followed by filterdouble <- doubletFinder(sc_tumor, PCs = doubletpc, pN = 0.25, pK = mpk, nExp = nexp_poi, reuse.pANN = FALSE, sct = TRUE) can be smoothly run.