You should change the "Identity Annotation (for technical replicates)" to blank.
That is currently set to "Condition", which is the same as the "Control Group Annotation", which means that Skyline thinks that all of your samples for a particular cohort came from a single individual and so there is no way to estimate variance across the population so there is no confidence interval or p-value.
It is important to use the Identity Annotation if you have technical replicates, because there will be lower variance among your technical replicates and if Skyline did not know that they came from the same individual, Skyline would underestimate the variance in the population and you would get a better p-value and smaller confidence interval than you should.
However, if you do not have technical replicates, and each of the Replicates in your Skyline document came from a different individual then you should leave Identity Annotation blank.
-- Nick |