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Published 20 hours ago • verified publisher icon sqjin

Cannot find obvious signalling

Open LucaTucciarone opened this issue 3 years ago • 2 comments

Dear CellChat developors,

I am Luca and I work in the Diabetes field. I have a big dataset with more than 30 samples from pancreatic islets (which are mainly based on beta cells) and I cannot seem to be able to find insulin signaling from beta cells. This is a little bit weird as I also run the same analysis on whole pancreas samples (12 samples) and I can see insulin signaling there where beta cells are not many at all!

I tried to play with the trim ball (right now I am going for trim=1 to have the whole df net list) and also using the population.size = TRUE (which usage I still completely do not understand. My single cell analysis is sorted and I guess I don't need to use it)

LucaTucciarone avatar Feb 10 '22 19:02 LucaTucciarone

@LucaTucciarone Please try this cellchat <- computeCommunProb(cellchat,type = "truncatedMean", trim = 0.1)

sqjin avatar Feb 10 '22 23:02 sqjin

I tried doing that but I still cannot find it. I am kinda confused honestly

LucaTucciarone avatar Mar 01 '22 22:03 LucaTucciarone