Hi,
I'm using Milo to perform differential abundance testing across different comparisons (e.g., WT vs Condition1, WT vs Condition2). Would you recommend constructing a single shared neighborhood graph for all comparisons, or building the graph separately for each one? I've tried both approaches, using a shared graph versus constructing them individually, and noticed slight differences in the results.
Hi,
I'm using Milo to perform differential abundance testing across different comparisons (e.g., WT vs Condition1, WT vs Condition2). Would you recommend constructing a single shared neighborhood graph for all comparisons, or building the graph separately for each one? I've tried both approaches, using a shared graph versus constructing them individually, and noticed slight differences in the results.