Subscript out of bounds - Running parameter sweep

[rahmaqadeer]

I am using Seurat version 5.0.1 and DoubletFinder_2.0.3 and encountering this error. Do you have any guides regarding this?

sweep.res.list_data_all <- paramSweep(data_all, PCs = 1:10, sct = FALSE)

[1] "Creating artificial doublets for pN = 5%"
Error in .subscript.2ary(x, , j, drop = TRUE) : subscript out of bounds
In addition: Warning message:
In LayerData.Assay5(object = x, layer = i) :
multiple layers are identified by counts.1 counts.2 counts.3
only the first layer is used

[bkheira]

Hi I am having the same issue, did you find how to do it ?

[Yijia-Jiang]

I encountered the similar issue

[yxsee]

I went back to using SplitObject instead of the Seurat v5 split layers and managed to get it working.

[aditisk]

I am encountering the same issue and already using SplitObject but it doesn't work for me. Does anyone have another solution? Thanks.