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Clustered Report values doesn't match with manual calculation

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Clustered Report values doesn't match with manual calculation Dhaval Patel  2025-07-22 15:12
 

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.
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.

This is also a continuation of my previous support request titled as “Live Report >Group Comparison on 2025-07-15 19:08.

Normalization method: Ratio to Heavy
 
 
Nick Shulman responded:  2025-07-22 22:55
When the normalization method for your group comparison is Ratio to Heavy, the Abundance values that you see in the Clustered report will be equal to the sum of the light areas divided by the sum of the heavy areas.
For the highlighted cells in your Document Grid, the light transition areas are:
173674
123794
128753
332098
and the heavy transition areas are:
2080409
1347270
472651
1301268
The ratio of those two sums is 0.1457 which is equal to the abundance value that you circled in the Clustered report.

You could also calculate this using the "Total Area" values for the two peptides in that protein.
The two light Total Area values are:
297378 + 460851
and the two heavy Total Area values are:
3428679 + 1773919
And the ratio of those two sums is also about 0.1457

You should add the "Isotope Label Type" column to your Document Grid report because it will make it easier to tell which rows are heavy precursors and which rows are light.

By the way, the Pivot Editor in Skyline might help you by grouping rows and calculating sums.
You can learn about the Pivot Editor here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=PivotEditor

-- Nick