Error running on cellbender adjusted counts

[yesitsjess]

Hi,

I've run cellbender on my data and read the filtered count matrix into R using Read_CellBender_h5_Mat from scCustomize and then converted that to a Seurat object using CreateSeuratObject.

I'm getting to following error when I run SCTransform:

Running SCTransform on assay: RNA
Running SCTransform on layer: counts.01. Control 1 UTC
vst.flavor='v2' set. Using model with fixed slope and excluding poisson genes.
Error in density.default(x = genes_log_gmean_step1, bw = "nrd", adjust = 1) : 
  'x' contains missing values

I've checked the cellranger documentation and the count data itself and they're integers so not log transformed. Lots of zero counts but there was before applying cellranger and SCTransform used to handle that fine.

Any help is appreciated. Thanks.

[saketkc]

What is the output of:

anyNA(object@assays$RNA@counts)