**50**wrote:

Hello,

I have a question concerning the difference between the linkage disequilibrium measures D' and r-squared. I know the formal definitions. But I have problems understanding the different concepts behind D' and r-squared? And what does it mean if D' is low and r-squared is high (and vice versa).

Thanks wim

**470**• written 3.9 years ago by wkreinen •

**50**

Yes, sorry. It is not a classical bioinformatic question. Thanks for the wikipedia link. Yes, I know that stuff. Unfortunately I did not understand it and obviously I could not make it clear what I did not understand ...

In my understanding of bioinformatics it is not a fault if one tries to explain some basic conceptual differences that make a difference in the end of the day. My impression is that D' and r-squared are used (quite often) arbitrarily.

I try to be more detailed in asking my question ...

D' and r-squared are different (and popular besinde others) approaches to normalise D. D' uses the theorectical maximum of D to do the normalisation, r-squared uses correlation coefficient. So far so good ... But I have problems to understand which conditions have an influence on choosing D' or r-squared as a parameter of ld. What are the important criteria to choose D' or r-squared? Maybe, this is the wrong forum to ask a question like this. If this is the case I wish to apologise. Anyway, I would appreciate if somebody could give me a productive hint.

All the best

Wim

50"In my understanding of bioinformatics it is not a fault if one tries to explain some basic conceptual differences that make a difference in the end of the day."

The problem is that the question isn't about bioinformatics at all. It's about population genetics. This group is for bioinformatics questions - issues specifically related to data handling, usage, and interpretation of biological datasets, not necessarily introductory population genetic theory outside the scope of a program. Also, you should consider posting a follow-up as a comment and not an answer to your question.

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