Comparison between Healthy vs Diseased

[trusha0911]

Hi Cyril! Many thanks for developing scDiffCom. It's such a helpful tool!

I have some very basic question. I want to compare healthy and diseased conditions from my dataset. In this case, should I have : cond1_name = "D", cond2_name = "H"

or

cond1_name = "H", cond2_name = "D"

This changes the upregulated and downregulated trends :)

And could you also kindly share your current email address for further communication? That would be great!

[CyrilLagger]

Hi, and thanks for the feedback!

The choice between the two cases is yours, but you need to be consistent when interpreting the results. When performing differential analysis, LOGFCs are computed as log(score(cond2_name)/score(cond1_name)). In other words, "UP"-regulated CCIs have a larger score in cond2_name.

So, if you choose

cond1_name = "H", cond2_name = "D",

then "up-regulated" means that the cell-cell interaction is stronger in the diseased condition.

Sure, you can ask more questions here or contact me at [email protected].

Best, Cyril