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czbiohub-sf / tabula-muris-senis

Tabula Muris Senis
http://tabula-muris-senis.ds.czbiohub.org
BSD 3-Clause "New" or "Revised" License
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No counts in AWS h5ad object #13

Closed gokceneraslan closed 4 years ago

gokceneraslan commented 4 years ago

AnnData file at AWS (https://cellxgene-example-data.czi.technology/tabula-muris-senis.h5ad) apparently does not have counts:

image

They also do not seem like log(TP10k+1). Do you mind adding a "counts" layer to the object which contains counts? Or is there another h5ad file which contains all cells across all tissues with counts?

gokceneraslan commented 4 years ago

Oh there is a .raw with counts, ok, please ignore then. It'd be great if you explain why adata_senis.X.expm1().sum(1) values are not <= 10000 though, if it's just np.minimum(log(tp10k+1), 10.0).