run RCTD for combined visium data

[gebdu]

Hi,

I have just started exploring RCTD. I have two 10x spatial visium slides from brain area. Each slide with 4 sections. So, total 8 samples. These are merged in Seurat. I will use a reference scRNAseq data to annotate cell types and proportions. Now is there any way to run RCTD for this combined set? Or do I have to run anyway individually and make images individually for each sample? Later I want to do Differential analysis.

myRCTD <- create.RCTD(query, SCreference, max_cores = 35)
myRCTD <- run.RCTD(myRCTD, doublet_mode = "full")

thanks,

[Chelsealai21]

Hi,

I am having the same issue. When I tried to run it with a merged Seurat object, it only runs RCTD on one of the slice and leaves the other slices grayed out.

[Cameron-Nguyen1]

Same issue as @Chelsealai21

Is the only solution to do as @gebdu mentioned and run RCTD per slide?

Thanks.