Working with multiple Visium HD samples.

[ChristelleBrest]

Hi Giotto team,
Congratulations and thanks a lot for your Giotto package and the workshop! I am working on two visium HD datasets. So I wanted to join them and I think, I have succeeded, but I wanted to know if you think that my pipeline is ok. First, I have created my two Giotto objects using the k100 resolution. Then I joined them using the « working with multiple samples » workflow and perform harmony correction. After clustering my cells, I run the Visium part II workflow.
Unfortunately, one of my two samples have a poor resolution and the clusters seems to be related with the samples.
Anyway, do you think that this approch can be validate?
Thanks a lot!
Christelle

[RubD]

Hi @ChristelleBrest, the approach is fine but combining samples from separate experiments is often times a challenge. Tools like Harmony (or others batch correction methods) can sometimes help but it's always important to be very careful with data interpretation. Ideally you want to consider optimizing your experimental design (e.g. multiplexing samples together or adding a reference sample if possible).