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carmonalab / ProjecTILs

Interpretation of cell states using reference single-cell maps
GNU General Public License v3.0
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What normalization has been done to data? #28

Closed njbernstein closed 2 years ago

njbernstein commented 2 years ago

I downloaded the seurat object from https://spica.unil.ch/refs.

I'm wondering for the following RNA data

b <- readRDS('/group/singlecell/mouse/andreata_2021_t_cell_atlas/ref_TILAtlas_mouse_v1.rds')
b@assays$RNA@data

is the counts normalized in the following way: log (1 + 10,000 x / S)? as describe in the paper

mass-a commented 2 years ago

Hello, for the TIL atlas, the count data was normalized using the NormalizeData function from Seurat with default parameters – this applies a log-normalization with scaling factor of 10,000 as you indicated.