Spatial transcriptome data, how to conduct multi sample analysis with biological duplication？

[maqingyue]

Hello, my data is from the spatial transcriptome. There are three biological repetitions in the experimental group and the control group respectively. Can I use three experimental groups to create a cellchat, three control groups to create a cellchat, and then two cellchat objects for multi sample analysis?

My main problem is that the spatial group data requires coordinates when creating a cellchat. When synthesizing three biologically duplicated samples into a cellchat, the superposition of coordinates may have an impact on subsequent analysis, as I see that the coordinates in the data structure of the cellchat are as follows.

If multiple sample analysis with biological duplication can be carried out in the space transcriptome, what should I do?

Thank you for developing this software. I look forward to hearing from you

[sqjin]

@maqingyue At this moment, I suggest to analyze the data by using only one replicate. It is a bit challenge to better capture the spatial relationships from different slices.

[maqingyue]

Ok, thank you for your answer.