Group Comparisons

Group Comparisons ssedigh2  2023-08-14 11:32

Hi ,

I am trying to do a group comparison for a peptides using my DIA data between a healthy and diseased group , for some reason the p-value for every peptide is showing 1, How can I trouble shoot that ?
also is there a way to export the peak areas ? the document grid doesn't have it .

Thank you

Nick Shulman responded:  2023-08-14 11:41
Can you send us your Skyline document?
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

If that .zip file is less than 50MB you can attach it to this support request.
You can upload larger files here:

-- Nick
ssedigh2 responded:  2023-08-15 11:04
Thank you for getting back to me I have uploaded the zipfile under name SS.

Nick Shulman responded:  2023-08-15 12:50
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
ssedigh2 responded:  2023-08-16 04:49
Thank you , but when I leave the annotation blank , it doesn't show me a group comparison grid anymore.
Nick Shulman responded:  2023-08-16 07:50
It works for me (see attached screenshots).

If it still does not work for you, then you should send me your new Skyline document.
-- Nick