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simonwm / tacco

TACCO: Transfer of Annotations to Cells and their COmbinations
BSD 3-Clause "New" or "Revised" License
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Raw counts data as reference or normalized data as reference? #2

Closed parkjooyoung99 closed 1 year ago

parkjooyoung99 commented 1 year ago

Hello,

I am using sc reference data processed via Seurat. While extracting expression data from Seurat object, I wonder which among raw counts and normalized data should I extract to use in tacco. Although the result did not deviate much from each other's, I wanted to be sure which is right.

Thank you!

simonwm commented 1 year ago

Hello, Generally tacco assumes that both the reference data and the data to annotate are given as raw counts. For the default settings it is expected that you don't see a lot of differences between normalized data and raw counts, but this can be quite different, especially for wrapped third party methods.

parkjooyoung99 commented 1 year ago

Thanks for your reply! Yes, I do see some differences between results but would select the one from raw counts.