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jcao89757 / SCINA

SCINA: A Semi-Supervised Subtyping Algorithm of Single Cells and Bulk Samples
http://lce.biohpc.swmed.edu/scina/index.php
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Error with SCINA command #25

Open martina811 opened 9 months ago

martina811 commented 9 months ago

Hello! I am trying to use SCINA with a very big dataset, it is ~ 25.000 genes and 80.000 cells. I Have a very large file of signatures downloaded from CellMarker (1600 signatures), but I filtered out all the signatures that do not have at least 2 markers genes that overlap with my expression matrix.

When I run SCINA i got sometimes the error "chol.default(theta[[i]]$sigma1) : 'a' must have dims > 0" and sometimes "Error in if (any(keep)) { : missing value where TRUE/FALSE needed".

I did many test with the same data, and for example I saw that with a exp matrix of 1200 genes and 2000 cells, the same signatures files always filtered with the same criteria, works with no errors.

So I want to ask if the size of the expression matrix could be a problem ? Because I did multiple test and I saw that often even with a signature file with many markers for each signature SCINA works with no errors.

Thanks a lot!

wtwt5237 commented 8 months ago

Hi @martina811

Yes, I am suspecting that the size of the dataset is causing this problem. Could you run your data in batches through scina, or just ignore the cells with low expression counts in all your analyses?

Thanks!

Tao