Two question regarding interpretation of the pathways having significant AUC for a specific LV

[ArashDepp]

Hi,
Very nice tool, but I have question to better interpret the results that I am getting.

Lets say, I run PLIER on a cohort of 100 samples, and observe that a specific pathway P1 is significantly aligned along the latent vector L1. On the other hand, we have pathway P2 which does not align with any of the latent vector (i.e AUC is very small). Then my question is, can I make any statement about the activity of pathway P1 and P2 in my 100 samples. In other words, is it correct to say that pathway P1 was active across my samples but pathway P2 was not active. Please let me know what is the right interpretation. I know that one can score P1 and P2 across samples using scores from B matrix (please correct if I am wrong), but can we bluntly say that if plier does not align a specific pathway along any of the latent vector, does it mean that pathway is inactive?

Second question is, how stable are the results if I add/remove new pathways to the prior information. If pathway P1 was significant on one of the latent vector when using N number of gene lists as prior information, will it be significant if we extend or shrink the prior information to N+n or N-n gene lists.

I would appreciate your response for these two questions

[ArashDepp]

Hi...thanks for promptly answering my other question, but could you please discuss this as well.