Thank you for uploading that .zip file.
The problem is that you have chosen "Condition" as the "Identity Annotation".
If you do not have technical replicates, then you should probably leave the "Identity Annotation" dropdown blank.
The problem with telling Skyline that "Condition" is the Identity Annotation is that it's telling Skyline that you only have samples from two human beings from each of the conditions. For this reason, Skyline is not able to estimate what the variation might be between different humans with the same condition, so the p-value ends up being 1.
If, instead, you changed the Identity Annotation to blank, Skyline would think that each of your replicates came from a different human being, and would be able to give you a p-value put confidence intervals around the fold change values.
-- Nick |