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SCTransform gives 'BLAS/LAPACK routine 'DLASCLS'" error #85
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I have not seen this error before. Can you share the data and the exact steps that led to this problem? In the meantime, make sure to install the latest sctransform version ( |
I am getting the same error on a visium dataset. Tried also method = 'glmGamPoi' with no success. This only happens to one out of 4 datasets that I am working with. Happy to share the data if necessary. What I ran so far: DBA_2J <- Load10X_Spatial(data.dir = paste0(data.dir,samples[3],"/outs")) Output: Session info: Matrix products: default locale: attached base packages: other attached packages: loaded via a namespace (and not attached): Matrix products: default locale: attached base packages: other attached packages: loaded via a namespace (and not attached): |
I'd be more than happy to have a look. If you want to share the data privately, use [email protected] |
@ahmedmahfouz Thanks for sharing the data. It turns out that there is a 'cell' with zero counts that is causing the problem. After loading the raw data, I recommend plotting some QC metrics and basic filtering. For example:
Of course, adjust these filter based on your data, and don't use strict filters if a signal of interest could be correlated with the QC metrics. |
Thanks Christoph, this worked. |
I'm trying to load multiple scRNA datasets, merge them, and run SCTransform, but I'm getting the following error:
If I try to follow up my SCTransform w/ the PrepSCTIntegration step with the following command
I get the following error:
My full code is :
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