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How to run the mellon on data obtained under different processing conditions #10
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Hi @minghao622! Thanks for your inquiry! We are currently working on establishing a differential abundance framework that will hopefully make this use case a lot easier. However, to answer your questions:
Please note, we haven’t established the units of the density values produced by mellon. While differences in the log-density values correspond to the predicted log-fold change of cell-state abundance, the absolute values should not be interpreted at this time Stay tuned for our upcoming work on differential cell-state abundance. |
Hello,
This is a very good tool! However, I have some questions while running the code.
1, I want to calculate the density changes of a specific cell type subpopulation under different treatments. Should I merge the data from multiple treatments and then run Mellon, or should I run Mellon separately for each treatment?
2, If I were to merge the data of multiple treatments for the process, would I need to integrate the data and then use the integrated PCA for running
palantir.utils.run_diffusion_maps(adata, pca_key="integrated_pca", n_components=30)
?Thanks for any advice.
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