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satijalab / sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression
GNU General Public License v3.0
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intermittent errors in SCTransform #75

Closed kmwinkley closed 3 years ago

kmwinkley commented 3 years ago

After the update to v.0.3.1, I occasionally get the following error:

Error in while ((it <- it + 1) < limit && abs(del) > eps) { : missing value where TRUE/FALSE needed Calls: SCTransform ... resolve.list -> signalConditionsASAP -> signalConditions

after doing some digging the error seems to be originating somewhere between the SCTransform and it's call to sctransform::vst

Namely, if I run the following code:

vst(seurat_object@assays$RNA@counts)

everything runs fine,

However this:

SCTransform(seurat_object)

will fail on some objects, but not others

ChristophH commented 3 years ago

Would you mind installing the develop version of sctransform (remotes::install_github("ChristophH/sctransform@develop")) and trying again? If you still see the error it would be great if you could share the seurat object. Which version of seurat are you using?

kmwinkley commented 3 years ago

Updating to the develop version of sctransform seems to have fixed the issue. Apologies for the slow response.