Using Proseg for tissue microarrays

[pravinvel98]

Hi I have been using Proseg for single tissue sections that have been processed by the Xenium analyser. I was wondering if Proseg will still run properly if the sample is composed of multiple individual tissue cores or some settings need to be changed. Thanks a lot!

[dcjones]

You certainly can use proseg on tissue microarrays, but there are a couple risks you should be aware of that may negatively affect the model.

• If the cores have very different z-coordinates (e.g. if some sections are thicker than others) that may diminish the usefulness of the 3d modeling proseg does.
• If the array contains radically different tissue types, they usefulness of proseg's gene expression model may be diminished. You can probably counter this by increasing the number of components in the mixture model, like --ncomponents 10 or --ncomponents 15.