Appropriate batch variable for specific experimental design

[lucygarner]

Hi,

I would like some advice on the appropriate batch variable for my experimental design.

I have samples from 8 different individuals - for 3 of these, I have cells from blood and liver, and for the other samples, I just have cells from the blood. After correction, I would expect liver cells from different donors to align and the same for blood. Since some of the donors lack liver cells, I would still expect there to be liver-specific clusters that contain 3/8 donors.

My current plan would be to use "donor" as the batch variable with a θ value of 0. Does this seem reasonable or what would you recommend?

Additionally, what is the best way to decide on the number of PCs to use as input to Harmony? Do you just decide based on a scree plot or is there a more statistically rigorous approach?

Best wishes, Lucy