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Hi!
Thanks a lot for this very useful tool.
I succesfully ran Augur on a large dataset ~70K cells using default parameters, I want to increase the number of celles in subsample_size to 1000-2000 cells to better capture the heterogeneity. I was wandering if you can give any recommendation about the fraction of cells per celltype and per condition that you think would be reasonnable to use.
Thank you!
The text was updated successfully, but these errors were encountered:
I essentially never change this parameter from its default values, but doing so should not impact your results very much. In Supplementary Fig. 6 of the Augur paper, we show that prioritizations are quite robust to the value of subsample_size - the main risk is removing cell types with too few cells from consideration.
I guess you are referring to Supp Fig7 (not 6), I saw this part but unfortunately it seems that the dataset tested is a bit small and it's difficult ton conclude whit subsample_size 50-100 .
Hi!
Thanks a lot for this very useful tool.
I succesfully ran Augur on a large dataset ~70K cells using default parameters, I want to increase the number of celles in
subsample_size
to 1000-2000 cells to better capture the heterogeneity. I was wandering if you can give any recommendation about the fraction of cells per celltype and per condition that you think would be reasonnable to use.Thank you!
The text was updated successfully, but these errors were encountered: