Combined Correctness
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Combined Correctness is a quality metric for 2D gel image analysis data. It is the product of spot detection correctness and spot matching correctness and can be applied independent of the software used to generate the data.
In short:
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Total Spot Correctness =
Correct / (Correct + False + Misshaped + Missing) |
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Pair matching correctness =
Correct / (Correct + Incorrect) |
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Combined correctness =
[Spot correctness] x [Pair matching correctness] |
Combined Correctness is expressed as a percentage score that allows us to draw statistically relevant conclusions about how good the 2D gel image analysis really is.
100% Combined Correctness basically means that you have made all possible discoveries, and have no false positives, in your results .
50% Combined Correctness means that there is potentially a lot more to find in your 2D gel experiment, and that many of the results you have will be errors.
For more detailed information about how Combined Correctness is calculated please refer to the reference material below.
Combined Correctness has been shown to be highly correlated to more true positives and fewer false positives in 2D gel image data.
A manuscript describing the research leading to Combined Correctness and it's implications for 2D gel based proteomics and co-authored by Ludesi as well as five independent proteomics groups has been submitted for publication.
Combined Correctness has been designed to be a generic metric, and can therefore be applied to any 2D gel software on the market today.
If you're curious as to how good your 2D gel image analysis really is, you can easily evaluate the Combined Correctness on your own data using the free GelIQ tool. Click here to go to the download page.
Reference material for Combined Correctness
Combined Correctness Can Enrich Proteomics
Genetic Engineering News, April 2008
How to Predict Discovery Potential and False Positives in 2D Electrophoresis Image Analyses
HUPO 2007 Poster
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Higher Combined Correctness always means more true positives:
Above Figure:For 11 independent sets of 2D gel projects two image analyses were preformed using different software. A Combined Correctness score was calculated for each analysis and the number of true positives in the image analysis data estimated. In all cases, data sets with a higher Combined Correctness score also displayed a higher percentage of true positives.
Higher Combined Correctness always means a lower false positive rate:
Above Figure:When the Combined Correctness is improved, the false discovery rate goes down. The Pearsson correlation coefficient for Combined Correctness’ correlation to false positives rate was 0.47, indicating a strong relationship between the two.
All data taken from the poster How to Predict Discovery Potential and False Positives in 2D Electrophoresis Image Analysis presented at the 2007 HUPO.
