Hi @vbhave. I don’t think anyone has addressed the exact question you are referring to; however, for your more specific question of how to get gene expression values for all genes in a single anatomical region, this has been addressed in another thread (which it seems you were also a part of!). If you do find that this type of normalization improves your analysis of the Adult mouse brain atlas data, please let us know (for example, by posting a link to your future publication in this thread).
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