Multiple xenium data analysis

[ilovegreentea]

Hello..

I going to analyse mutiple xenium data set.
so i just read each Xenium data and merged with merge() function.
after that, i processed the data.

but i'm wondering how plotting ImageDimplot the data which I want to see.
and i have problem at subsetting data.

Error messege is below

subset(merge, sample_name != 'yet')
Error in as.Graph():
! Please provide rownames to the matrix before converting to a Graph
Run rlang::last_trace() to see where the error occurred.

who have any idea to analysis multiple xenium data set, please give me any advice.

thank you.

[RajneeshSrivastava]

Seurat Team,
Just curious, if there is a solution for merging multiple xenium dataset, as issue raised by @ilovegreentea

[ilovegreentea]

I Found some solution below. Using subset_opt function

#8848
#7947 (comment)

[ramosemi]

Hello Seurat team,
I would like to analyze 4 xenium samples and perform a pseudobulk analysis and compare expression of a few genes (PTX3 for example) in the fibroblast population of each sample. Do you have a general recommendation on how to perform pseudobulk analysis for multiple Xenium samples?