In what situations is 'outer' typically used when using anndata.concat()?
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5 weeks ago
Spring • 0

Hi, I have 9 samples with identifiers starting with SRR24304... I calculated the HVGs (highly variable genes) for each sample and then combined them using adata = anndata.concat(adata_list, join='inner'). However, only about 300 genes remained (the intersection), which is concerning as many genes were discarded. Would it be problematic to use 'outer' join instead of the default 'inner' join? In what situations is 'outer' typically used? Thanks.

concat anndata scanpy • 116 views
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