Merging Xenium objects with 2 conditions and 3 replicates Analysis

[mckoch234]

Hello,

I have made a list of cellchat xenium objects by replicate and merged them into one cellchat. I have tried doing cellchat <- identifyOverExpressedGenes(cellchat ,group.dataset = "seq_folder", pos.dataset = pos.dataset, features.name = features.name, only.pos = F, thresh.pc = 0.1, thresh.fc = 0.05,thresh.p = 0.05, group.DE.combined = FALSE) to do differential expression analysis between conditions however no matter how I change the parameters identifyOverExpressedGenes compares them by replicates not by condition, even when i have condition in the meta data of each cellchat object in the merged object. How do I overcome this or merge the replicates in a way where I can compare them by condition, or set so when I make graphs and such it does it by condition not replicate? The tutorial did not help much as it only did 1 replicate per condition not multiple.

[mckoch234]

Am I supposed to merge the spatial seurat or sce objects by condition first then make a cellchat for each condition and merge those? I do not believe spatial objects can be combined in that way.

[Sophielsn]

Hi. I am working on integrating the spatial cellchat step now. Do you have any updates?

[mckoch234]

Hi. I am working on integrating the spatial cellchat step now. Do you have any updates?

I focused instead on only 2 samples to make the merged cellchat and did identifyoverexpression between those. I was not able to figure out how to handle replicates. I cannot merge spatial objects without losing the spatial information.