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Danko-Lab / BayesPrism

A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression
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Example about Computing z-scores of signature genes for Z of the cell type of interest. #85

Closed 1667857557 closed 3 months ago

1667857557 commented 4 months ago

Hi, Dr.Chu

Thank you for your excellent work. Could you provide some examples and code related to the downstream analyses, specifically "Computing z-scores of signature genes for Z of the cell type of interest"? It would be very helpful for our work. Thanks in advance!

Best, Yu-Feng Huang

tinyi commented 4 months ago

Hi Yu-Feng,

Thank you for your interest in our method.

Could you kindly let me know which figure(s) in our manuscript were related to the z-score you were referring to? Many thanks.

Best,

Tinyi

On Wed, May 15, 2024 at 6:11 AM Yu-Feng Huang @.***> wrote:

Hi, Dr.Chu

Thank you for your excellent work. Could you provide some examples and code related to the downstream analyses, specifically "Computing z-scores of signature genes for Z of the cell type of interest"? It would be very helpful for our work. Thanks in advance!

Best, Yu-Feng Huang

— Reply to this email directly, view it on GitHub https://github.com/Danko-Lab/BayesPrism/issues/85, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4NHSZHZI5DF2TTCYCMK23ZCMYE3AVCNFSM6AAAAABHX23ZA6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGI4TONBUGMZTAOA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

1667857557 commented 4 months ago

Hi Tinyi,

The step titled 'Computing z-scores of signature genes for Z of the cell type of interest' was mentioned under the 'Downstream Analysis' section in the tutorial_deconvolution.html file you provided.

Best, Yu-Feng Huang

tinyi commented 4 months ago

Hi Yu-Feng,

z score is simply (z_i - mean(z)) / sd(z). you can use the scale function in R to compute this.

Best,

Tinyi

On Mon, May 20, 2024 at 9:18 PM Yu-Feng Huang @.***> wrote:

Hi Tinyi,

The step titled 'Computing z-scores of signature genes for Z of the cell type of interest' was mentioned under the 'Downstream Analysis' section in the tutorial_deconvolution.html file you provided.

Best, Yu-Feng Huang

— Reply to this email directly, view it on GitHub https://github.com/Danko-Lab/BayesPrism/issues/85#issuecomment-2121522588, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4NHS54U5TWBDKFEULAKDTZDKOFVAVCNFSM6AAAAABHX23ZA6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRRGUZDENJYHA . You are receiving this because you commented.Message ID: @.***>