I am in love with the “Differential search” function for the ISH data of the mouse brain and I wish to write a Python script that reproduces the search (eg) below programmatically.
I then found this very helpful doc that allows me to do so, but my results are not consistent with the website (I find more genes than when I query via the Allen website, although structures and dataset are the same).
I think that this is due to the threshold parameters: in the query to
system :: mouse_differential I have 4 different thresholds: start/end threshold for either target or contrast. In the website, I only have one slider that controls one expression threshold that ranges from 0 to 7.
- Could you please tell me how to reproduce differential gene search via URL/API that are consistent with Allen website?
- I guess that means, could you tell me the 4 values of the thresholds that you use in Allen website ?
- Would you recommend any particular threshold value to get biological significant results?
Thank you very much,