Error calling estimateExpressionShiftMagnitudes function with Seurat object

[mkazanov]

Hi, I am trying to use cacoa with Seurat object and to follow vignettes.
Code below failed on estimateExpressionShiftMagnitudes function with the following error message:

Error in FUN(X[[i]], ...) : 
  no slot of name "counts" for this object of class "Assay5"

cao <- Cacoa$new(so, sample.groups=sample.groups, cell.groups=cell.groups, sample.per.cell=sample.per.cell, 
                 ref.level="control", target.level="case")

cao$estimateCellLoadings()
cao$estimateExpressionShiftMagnitudes()

[rrydbirk]

Hi @mkazanov

Sorry for the late reply. I assume you're using Seurat5. I know that the new version created a lot of issues with other packages. We didn't test Cacoa on the new version yet, but we'll add it to our to-do.

/Rasmus

[chilampoon]

hi I encountered the same issues and this is my quick workaround #53 (comment). it works properly in my end.

[luostrowski]

Hi! Are there any updates on this? I'm having the same problem with Seurat v5.