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atarashansky / SAMap

SAMap: Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms.
MIT License
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The gene expression levels after SAMap-integrated are all greater than 0 #116

Closed HYJ-hh closed 1 year ago

HYJ-hh commented 1 year ago

Hello, I noticed that after integration with SAMap, the gene expression levels are all greater than 1, which is usually greater than 0, I can't find a specific reason.

atarashansky commented 1 year ago

Hello, nice observation. If you processed the data with SAM (e.g. loaded raw h5ad's into SAMAP), then that's why. SAM preprocessing function zeroes out expressions less than 1 by default.

HYJ-hh commented 1 year ago

Thank you. In that case, perhaps I should go and learn more about SAM.