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digitalcytometry / ecotyper

EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
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question regarding abundance table #51

Closed kaizen89 closed 1 year ago

kaizen89 commented 2 years ago

Hi, I am wandering what does the abundance table exactly refer to, is it abundance of cell states among each cell type or is it among all cells. On my data I am not getting a sum of abundance =1 in either case. Could you please clarify this point? Thanks!

kaizen89 commented 1 year ago

Anyone could please comment on this?

kaizen89 commented 1 year ago

Sorry to insist but this question is really important.

BALuca commented 1 year ago

Hi,

Apologize for the confusion and delay. The abundance table refers to the relative abundance of cell states within each cell type. They do not sum up to 1 because the poor-quality states from each cell type are filtered from the analysis, but their share of abundance is not re-distributed to the remaining states.

Best, The EcoTyper team