Entering edit mode
10.1 years ago
LauferVA
4.8k
I am writing to find out what the most common or most widely accepted algorithm for calculating Meff, or the number of linkage independent effective SNPs.
I am authoring a research article on a study conducted via the immunochip, and have found SEVERAL articles that use widely varying figures for Meff, everything from LD independent ~67000 to ~14000 SNPs. Needless to say, since these numbers differ by a factor of 4 or so, and since that directly affects the Bonferonni adjusted threshold, making the wisest choice here is important.
To help me make that choice, I was hoping to ask 3 questions:
- Is there a most common way of doing this for Ichip studies?
- Many times, expert opinion converges on a solution, but that convergence is not reflected in the literature for several years. At this point, is it already clear which solution is the most accurate for estimation of Meff?
- Pursuant to answering 1 and/or 2., are there any good review articles that could help me understand the assumptions on which these rely?