Normalization on data set with two panels

[LisaMarieKronstad]

I ran a 9 donor, 9 day experiment on Helios with half samples stained with one panel and half with a separate panel, both with DVS beads. I used the bead-normalization tool to normalize the files all at once - is there any reason that this would be an issue? Should I stead normalize the samples with each panel separately? Thank you.

[zbjornson]

I don't think there's any issue with that (does your data look alright with a quick sanity-check glance?). However, it's also probably not that important to normalize them together since the point is to make antibody signals consistent within a panel.