• Sign In
  1. Requests

Live Report > Group Comparison

support

View Request

view list print
Live Report > Group Comparison Dhaval Patel  2025-07-15 09:58
 

Hi,

I performed a simple group comparison between the control and treatment groups at the protein level, which generated a table showing fold changes and adjusted p-values.

Is there a way to quickly extract the actual intensity or abundance or ratio values that were used behind the scenes to calculate these results?

Our collaborator would like to have these values in Excel format to cross-verify the statistical findings independently.

I’ve attached screenshots of the analysis settings for your reference. Please let me know if you need any additional information or clarification. Happy to share actual file if needed.

Thank you,
Dhaval
 
 
Nick Shulman responded:  2025-07-15 11:20
At the top of the "Exp 17-Semgalutide:Grid" window, there is a button that says "Reports".
If you push that button and choose "Clustered" then the grid will change to show you per-replicate abundances.
When you choose the "Clustered" report, Skyline also colors the cells according to their values.
Unfortunately, the only way to turn off those colors is to customize the report, and give it a different name. Once you've renamed the report, you can use the "Cluster Grid" menu item on the third button from the top left corner to turn off the colors on the grid.
-- Nick
 
Dhaval Patel responded:  2025-07-16 12:40
Thank you. That information is indeed helpful.
Also, does it perform a paired or unpaired t-test? Is there any skyline documentation or help guide to refer it?
 
Nick Shulman responded:  2025-07-16 12:53
Skyline does not do paired t-tests.
If you want to do a paired t-test you should use MSstats Shiny.
If MSstats notices that the same BioReplicate value can be found in more than one Condition, then MSstats does a paired t-test.
-- Nick
 
Dhaval Patel responded:  2025-07-16 13:31
Perfect. I need an unpaired t-test only.

While cross-checking the values from the Clustered Report against those I manually calculated from the Document Grid, I noticed they don’t match.

I’m certain I’m missing something in the process but haven’t been able to pinpoint the mistake. I’ve attached a PowerPoint file with my specific question and a screenshot to help illustrate the discrepancy.

Your guidance would be highly appreciated. Thank you once again for your continued support.
 
Dhaval Patel responded:  2025-07-22 15:01
Hi Nick,
I was wondering if you get a chance to review my above response and help me with that query?

Thank you
Dhaval