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How to use MiloR after subsetting the cell types from total cell types? #337
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Hi @mainharryHR - the main issue here isn't to do with Milo. If the total T cell population is expanding relative to the stromal cells then when you subset to just the T cells you have removed the major difference, and it's just a difference in total number of cells (which is a normalising factor in the NB-GLM). Using Milo2.0 from Bioc 3.19, you can pass an explicit |
Thank you very much for great suggestions. It works. I input the total cell number per sample by using |
@mainharryHR - you're asking me to interpret your results. You've noted there are heterogeneous changes in your annotated populations, so that's now up to you to interpret. |
Thank you very much for confirming my guess. I appreciate your kind help! :) Have a nice day! |
Dear MiloR team,
Thanks for the nice packages.
Recently, I am thinking how to use MilorR properly after subsetting the cell types from total cell types. In my case, whole T cells are expanding proportionally out of stromal cells and epitheliums in disease conditions. After subsetting the T cells for detailed annotations and analysis, there is no significant expanding in disease conditions any more. I am wondering how to use MiloR to analyse the cell abundances after subsetting the cells from total cell populations by accommodating the cell compositions before subsetting.
I am wondering if there is parameter we could adjust in order to accommodate the information from previous layer (whole tissue data). For example, we observe T cells are expanding 1.5 times out of total cells.
I am not sure I describe my questions clearly.
Thank you very much.
Best,
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