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rmarkello / abagen

A toolbox for working with Allen Human Brain Atlas microarray expression data
https://abagen.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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The problem of abagen obtaining the number of AHBA genes #228

Closed zzcpage closed 7 months ago

zzcpage commented 8 months ago

Hello, I encountered a question while using Abagen to obtain the expression of AHBA gene set in the brain. I hope you can provide an answer. It seems that the number of genes I extracted through Abagen is only 15633. But most of the literature I have read mentions that the number of AHBA genes obtained exceeds 20000. What is the reason for this?

liuzhenqi77 commented 7 months ago

Hi,

Abagen aims to provide standardized workflows and to avoid common pitfalls for people working with AHBA, so a number of best practices were implemented. Not all the genes were retained. Meanwhile, many different processing options can be explored.

Please refer to relevant publications for details.

https://elifesciences.org/articles/72129 https://doi.org/10.1016/j.neuroimage.2019.01.011

Thanks! (Feel free to reopen if you have further questions.)