Histocat - Differential cell neighborhood analysis
Posted: Tue Apr 23, 2019 11:36 pm
Hi all, hope you are well!
We have 70 samples analyzed by IMC, and they are graded 1-4 in disease severity. Is there a way to see if cell types interact differently between the severity stages?
For example, should we tsne+phenograph on all the samples together, and then run the neighborhood analysis on the different severity groups separately? So we would have 4 neighborhood analyses, then compare the significant interactions among them somehow.
Our hypothesis is that inflammatory cells may interact with structural cells more as the disease severity increases, leading to tissue destruction.
Any thoughts on this would be much appreciated!
Best,
Steve
We have 70 samples analyzed by IMC, and they are graded 1-4 in disease severity. Is there a way to see if cell types interact differently between the severity stages?
For example, should we tsne+phenograph on all the samples together, and then run the neighborhood analysis on the different severity groups separately? So we would have 4 neighborhood analyses, then compare the significant interactions among them somehow.
Our hypothesis is that inflammatory cells may interact with structural cells more as the disease severity increases, leading to tissue destruction.
Any thoughts on this would be much appreciated!
Best,
Steve