DoubletFinder error

Question

[marco.barr]

Hello everyone, I am performing cell doublet prediction in scRNA analysis with DoubletFinder. However, I am encountering this error.

sweep.list <- paramSweep(filtered_seurat, PCs = 1:min.pc)

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_CTL counts_PT
only the first layer is used

Layers(filtered_seurat)
[1] "counts_CTL" "counts_PT"  "data_CTL"   "data_PT"    "scale.data"

I have already successfully completed the analysis up to FindCluster. How can I resolve this? Should I perhaps initialize a list where I perform the DoubletFinder functions and then filter for each layer? And what type of error is the first one instead? This is the first time it has appeared in my analysis. Thank you very much for your help.

[fracarb8]

The error is telling that there are multiple layers available (seurat v5 I assume). Try by joining the layers (JoinLayers())

Answer 1

[tothepoint]

Based on the error there may be issue with default assay or PC are not been compute properly. Can you check default assay for your filtered_seurat object and also PC number if that is coming from right layer/slot?

Something like: length(filtered_seurat@reductions$[e-mail][1, ])

[marco.barr]

Thank you very much for the response. Your command returns:

length(filtered_seurat@reductions$[e-mail][1, ])
[1] 20

I am not sure if the solution as suggested above is correct because my data is not replicated but different, like a control and a patient. I welcome any suggestions.