I have data coming from another analysis merged with loom data with spliced/ unspliced counts. After merging adata with loom file, and apply scvelo.pp.filter_and_normalize, it notices that adata X was preprocessed and doesn't normalize it but logarithmizes anyways. It causes X to be logarithmized twice, once in the earlier analysis and once with scvelo. Is it possible to apply layers_log={'X', 'spliced', 'unspliced'} similar to what was discussed here: question about normalization. In a way that I will be allowed to decide which layers to be logarithmized?
Or, alternatively, would it be okay to do that: Applying filter_and_normalizeonly to loom file and merge afterwards such as:
Edit: After some search, I fell like logarithm is already only applied to X to begin with. Is it true? Then when I set log to False, problem will be solved.
Hi, I have a question/request:
I have data coming from another analysis merged with loom data with spliced/ unspliced counts. After merging adata with loom file, and apply scvelo.pp.filter_and_normalize, it notices that adata X was preprocessed and doesn't normalize it but logarithmizes anyways. It causes X to be logarithmized twice, once in the earlier analysis and once with scvelo. Is it possible to apply
layers_log={'X', 'spliced', 'unspliced'}
similar to what was discussed here: question about normalization. In a way that I will be allowed to decide which layers to be logarithmized?Or, alternatively, would it be okay to do that: Applying
filter_and_normalize
only to loom file and merge afterwards such as:Thank you very much for the scVelo :)
Edit: After some search, I fell like logarithm is already only applied to X to begin with. Is it true? Then when I set log to False, problem will be solved.