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Danko-Lab / BayesPrism

A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression
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question about input data in BayesPrim #9

Open huawen-poppy opened 2 years ago

huawen-poppy commented 2 years ago

Hello. Thank you for the amazing tool BayesPrim. I am wondering if I have bulk RNA seq data under A, B, C, and D conditions. But I only have the single cell sequence data under condition A. Can I still feed the BayesPrim with all the data to infer the cell type composition in bulk seq data under condition B, C, and D?

tinyi commented 2 years ago

Hi. Thank you for your interest in our work.

Although BayesPrism is robust to biological variation in the context of tumor heterogeneity, it is hard to predict the extent to which your experimental condition will affect the performance of BayesPrism. This can be highly problem-specific, which ultimately boils down to the question of how much information from scRNA-seq in condition A is retained in other conditions. That being said, I would recommend the use of highly cell-type specific markers (computed from the scRNA-seq of condition A), by implicitly assuming that these marker genes retain their cell type-specificity in other conditions.

Best,

Tinyi

On Tue, Aug 9, 2022 at 1:58 PM huawen-poppy @.***> wrote:

Hello. Thank you for the amazing tool BayesPrim. I am wondering if I have bulk RNA seq data under A, B, C, and D conditions. But I only have the single cell sequence data under condition A. Can I still feed the BayesPrim with all the data to infer the cell type composition in bulk seq data under condition B, C, and D?

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