Clarification about prediction target

3rd (Public) Challenge
1

I followed the provided code that create batch effect correction data, and then compute the Y. However there could be negative value for Igg, such as subject ID 10, specimen ID 77, timepoint0 IgGPT -0.024370729.

Then why compute fold-change it would be negative.

Should I use the original data to compute the prediction target?

3

Hi @timtsang ,

Apologies for missing your post earlier. Batch correction methods, like ComBat, often introduce negative values due to centering and scaling, particularly for measurements close to zero. For fold-change tasks, I would use the original normalized data to avoid issues with negative values.

I would also like to invite @all contestants to share insights or suggestions on how to better handle negative values in such cases.

Best,
Pramod