Question on gene filtering for correlation between malignant cell expression and query cell type fraction

[fanying2015]

Hi Tinyi, Thank you for providing the nice tool and tutorials!

I'm also interested in correlation between malignant cell expression and query cell type fraction. Could you provide the scripts how you filter out the genes? I'm reading Supplementary Note 9 but still not sure how, especially on the 'regress-out filter'.

Thank you!

[tinyi]

Sorry for the delay. I have been traveling recently, and will get back to you as soon as I can.

On Mon, May 12, 2025 at 9:57 AM fanying2015 @.***> wrote:

fanying2015 created an issue (Danko-Lab/BayesPrism#117) https://github.com/Danko-Lab/BayesPrism/issues/117

Thank you for providing the tool and tutorials, I'm also interested in correlation between malignant cell expression and query cell type fraction. Could you provide the scripts how you filter out the genes? I'm reading Supplementary Note 9 but still not sure how, especially on the 'regress-out filter'. Thank you!

— Reply to this email directly, view it on GitHub https://github.com/Danko-Lab/BayesPrism/issues/117, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4NHSZK5LH6XMM3QCHYKL326CSEXAVCNFSM6AAAAAB4575TE6VHI2DSMVQWIX3LMV43ASLTON2WKOZTGA2TOMBXGY2TANA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[tinyi]

Sorry for the delay. Here are the functions needed to run the regress-out filter. Please refer to the get_p_exp_theta, which is the main function that computes the p-value.

https://github.com/tinyi/BayesPrism_downstream_analysis/tree/main/Regress-out%20filter

[fanying2015]

Thank you for uploading the scripts! I really appreciate your help!