Suoqin Jin

@strawberry098 You can check the calculated probabilities and associated p-values. cellchat@net$prob and cellchat@net$pval give these two results. I just cannot imagine there is no values after running `cellchat

@anemartinezlarrinaga2898 Sorry for the late. I was thinking about the point you bring out. We identify DEG between different cell groups for each phenotype. I might more or less understand...

@CroixJeremy2 Thank you!

@PNA743 You can check our paper on the definition of the standard permutation test. P-values of 0 means none of the permutations have higher interaction probability than the observed data...

@masa187 The interactions with p-value = 0 are definitely needed for further analysis as they are the most significant ones. p-value=0 is simply 0. The comment `p-value < 0.01 is...

@apal6 @JoyOtten The plot shows the complement and GAS are comparable in both conditions and slight increase in LS conditions.

@laijen000 Can you check the average expression of signaling genes of interest, e.g, `computeAveExpr(cellchat, features = c("CXCL12","CXCR4"), type = "truncatedMean", trim = 0.1)`.

> > Hi@MMriran，in fig2b, slightly higher scores of both Sender and Receiver for FIB-D suggest that FIB-D is the autocrine signaling. The same case is for MYL-A population. > >...

@sandhusumiti Do you also extract the data from scanpy?

You may have to run `future::plan("multiprocess", workers = 4) # do parallel options(future.globals.maxSize = 1000 * 1024^2)` On Fri, Jun 2, 2023 at 6:09 PM VaiskiVemmel ***@***.***> wrote: > Hi....