Integration of NanoString CosMx FOVs

Question

[solo.albif]

Hi,

I'm working with a dataset generated using the NanoString CosMx platform with the 1000-gene panel. Since CosMx analyzes tissue samples using multiple adjacent fields of view (FOVs), I was wondering whether batch effects can occur between different FOVs, even when they are part of the same run.

Is it possible to observe batch effects between FOVs in this context?

Answer 1

[Bastien Hervé]

To have a more suitable answer to your question I would have a look at how the readout of RNA probes from CosMx is done.

On the same run, I don't see any particular reason why the capture of probes on the side of the slide would be more problematic than on the center, or the other way around, or from top to bottom.

However the field is quite new, so maybe we will find out in a couple of weeks, some biais between FOVs.

One can also plot cells on a UMAP and check for potential clusters specific to a FOV, it will give some hits.