Error in .subscript.2ary(x, , j, drop = TRUE) : subscript out of bounds

[Yijia-Jiang]

Hello, I am trying to use doubletfinder in seurat v5, and met the following error when running sweep.res.list <- paramSweep_mod(seurat_obj, PCs = 1:30, sct = T). Could you help fix this issue?

Error: Error in .subscript.2ary(x, , j, drop = TRUE)

Thank you very much!

[biomarkerman]

Same issue. I thought it worked perfectly in the previous release with the same dataset I have now. Is there a way it can be adjusted easily? Thank you!

[eegk]

Edit: ok I fixed the issue by running DF on individual samples. The problem is that when editing V5 seurat, layers move around objects and structure changes. doubletfinder cant find/identify where the new objects are and it fails. Specially with complex experiments. You have to use sample by sample. @biomarkerman

[IrinaVKuznetsova]

the same error here. Seurat v5 and DoubletFinder v.2.0.4 trying to run DF on individual samples as advised

[yxsee]

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