Question about the input of the kinaseSubstrateScore function

[iamagerm]

Hello, I am a new PhosR package user and I would like to make a question about it.

I generated the matrix of kinase-substrate relationship scores for my dataset, and to do this I used the matrix of phosphosites generated like this:

1)I read in R a file containing phosphosites and their intensities, not log2 transformed, like this:

and I have 8 replicates for B2 and also for WT

2)I filtered, imputed and then I selected from that matrix only those phosphosites that resulted differentially regulated from a t-test
3)I standardized the matrix
4)And then I gave this standardized matrix to the kinaseSubstrateScore function.

I have a question: in point 1), do I have to transform the intensities in log2 or should I work with intensities like I did in order to generate a correct matrix?

I have also a question about the algorithm that generates the matrix: is the profile matching score calculated considering the value of the phosphosite in each sample?

Thank you for your consideration.