No User Specification of Samples' Conditions

[DarioS]

The journal article refers to conditions a lot. For example, if there are I conditions, J experiments and K peptides then Residual Sum of Squares has IJK -I - m degrees of freedom. But, looking at the Usage section of the ReadMe file, there is no input parameter to define each sample's condition (my guess is values like "Healthy" and "Cancer"). Where has conditions gone or am I misunderstanding?