Group Comparison with multiple parameter david hoi  2021-02-24

Hello everybody,

I am trying to set up a group comparison were I want to compare a treatment vs a control at several time points in triplicates which I annotated . However, the group comparison only allows for annotation of 2 parameters such as treatment vs control and replicate, leaving me no option to also select the time points. Is there a way how I could overcome this and combine the analysis or will I have to do this separately?

Many thanks in advance,

Nick Shulman responded:  2021-02-24
For Skyline group comparisons, you always have to designate one replicate annotation value as the control group, and the fold changes are calculated relative to that control group.
You are allowed to leave the "Value to compare against" value blank, in which case Skyline will give you different fold change values for each of the other groups compared to that one control group.

In your case, I think you really will need to create two separate Group Comparison definitions: one to compare group A against group B, and one to compare group C against group D.

-- Nick