Group Comparisons

Group Comparisons ssedigh2  2023-08-22 05:25

Dear Skyline team ,

I am trying to do group comparison , and for some peptides even though it shows in the peak areas-replicate comparison that it is lower in my ICM condition than NF condition , when I do the group comparison , it shows that it has a positive fold change ( screen shot attached ) I was wondering can you help me figure out what I am missing here ?


Nick Shulman responded:  2023-08-22 06:08
Which normalization method is your Group Comparison using?
The Peak Area Replicate Comparison graph in your screenshot is showing you unnormalized values. In the Skyline document that you sent me last week your Group Comparison was using the normalization method "Equalize Medians".

You can right click on the Peak Areas graph and choose to display a different normalization method.
In your Skyline document, when I choose "Normalized To > Equalize Medians" on the Peak Area graph, all of the bar graphs except one seem to disappear.
The reason that this happens is that you have one replicate "S17" where more than half of the transition peak areas are zero.
For this reason, when Skyline normalizes observed values to the median peak area, the normalized values for the replicate S17 end up being much much larger numbers than for all of the other replicates, and so you only end up being able to see one bar in the Peak Area Replicate Comparison bar graph.
-- Nick
ssedigh2 responded:  2023-08-22 07:17
Thank you , I understand , how can I discard S 17 from my calculations completely ?
Nick Shulman responded:  2023-08-22 07:29
The easiest way to get rid of S17 would be to go to "Edit > Manage Results" and remove that replicate.

Alternatively, you could change the "Condition" value for that replicate to something else so that it does not get included with Group Comparisons involving the other replicates.
-- Nick