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)

[mdpatric]

Was anyone able to find a solution to this?

[yesitsjess]

What is the output of:

anyNA(object@assays$RNA@counts)

This is FALSE for each layer and also FALSE if I join the layers
I didn't find a solution - I'd still be interested in one

[mdpatric]

What is the output of:

anyNA(object@assays$RNA@counts)

This is FALSE for each layer and also FALSE if I join the layers I didn't find a solution - I'd still be interested in one

In some versions of cellbender 3.0.0 and 3.1.0 there is a bug that outputs negative values in the count matrix. Check for negative values in your output matrix. Sadly to fix this you will have to rerun cellbender on the master branch download or they have some proposed ways to recover messed up matrixes on the cellbender github if you have your checkpoint files.

[yesitsjess]

What is the output of:

anyNA(object@assays$RNA@counts)

This is FALSE for each layer and also FALSE if I join the layers I didn't find a solution - I'd still be interested in one

In some versions of cellbender 3.0.0 and 3.1.0 there is a bug that outputs negative values in the count matrix. Check for negative values in your output matrix. Sadly to fix this you will have to rerun cellbender on the master branch download or they have some proposed ways to recover messed up matrixes on the cellbender github if you have your checkpoint files.

Ok yes I have negative values - thanks for the pointer! I'll try rerunning it with a new version of cellbender (urghhh, it takes ages). Thanks again.

EDIT: there's a command in README to allow just a partial rerun and salvage v0.3.1 https://github.com/broadinstitute/CellBender/blob/master/README.rst