You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
from the matrix P(spatial spots X cells) I'd like to get the percentages for each cell type per spot.
Starting from the probability matrix spatial spots X cells, I was thinking to proceed in this way:
assign to each cell a known cell type
calculate the median probability per cell type, obtaining the matrix spatial spot X cell type
normalize each row value on the rowSum
(optional) filter out values < 0.01 and rescale percentages similarly in (3)
Do you see any pitfalls in this methodology? Would you recommend any another strategies to calculate cell type percentages per spot? I observed that generalising on cell types starting from individual cell probabilities gives me slightly better predictions rather than calculating the probability for each cell type, but maybe it's data-dependent.
Best,
Carlo
The text was updated successfully, but these errors were encountered:
In order to get the percentage of cell types per spot I would deconvolve. This means that you need to have prior information of how many cells you have per spot (eg via segmenting the corresponding H&E, if using Visium). You then need to deterministically assign the cells within the spot, then compute the percentage.
Alternatively, you can attempt the strategy you described although I am not entirely sure results will be consistent. Can you describe me in more detail how you want to do (1) and (3)?
Hi,
from the matrix P(spatial spots X cells) I'd like to get the percentages for each cell type per spot.
Starting from the probability matrix spatial spots X cells, I was thinking to proceed in this way:
Do you see any pitfalls in this methodology? Would you recommend any another strategies to calculate cell type percentages per spot? I observed that generalising on cell types starting from individual cell probabilities gives me slightly better predictions rather than calculating the probability for each cell type, but maybe it's data-dependent.
Best,
Carlo
The text was updated successfully, but these errors were encountered: