Hi there,

I am working on a Xenium dataset that includes two housekeeping genes in the panel. I wonder how to make use of those genes. My ideas were to use them somehow in the normalization (as normalization factors?) and/or for doublet detection. Indeed those could provide a baseline of transcripts level useful to compare cells. This is especially important as my Xenium samples were generated from sectioning slides of 5um which will contain some cells entirely and some others are expected to be cropped.

Anyone ever used housekeeping genes for such purposes?

Thank you very much for any insights!