mlma vs mlma-loco for lambda

john8604
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mlma vs mlma-loco for lambda Mar 3, 2016 8:28:58 GMT via Tapatalk

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Post by john8604 on Mar 3, 2016 8:28:58 GMT

Hi, Jian Yang

I am analyzing GWAS for growth rate (about 1,000 pigs).

I know that MLM-LOCO analysis more powerful as compared with the MLM analysis including the candidate.

But when I use "--mlma-loco" option for GWAS, lambda increase (λ=1.27) Unlike "--mlma" (λ=1.01).

In this situration, is "--mlma" moreaccurate than "--mlma-loco"?

Otherwise, should I use "--mlma-loco" option, out of lambda increasing?

Jian Yang
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mlma vs mlma-loco for lambda Mar 3, 2016 12:05:53 GMT john8604 likes this

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Post by Jian Yang on Mar 3, 2016 12:05:53 GMT

Please see www.nature.com/ng/journal/v46/n2/full/ng.2876.html

MLMA-LOCO is meant to be more powerful than --mlma. However, it seems that your lambda value is a bit too high given the sample size. Sorry, I can't give any advice without seeing all the details. If you were to be conservative, you might use --mlma.

john8604 New Member Posts: 2	mlma vs mlma-loco for lambda Mar 4, 2016 0:07:11 GMT via Tapatalk Quote Select Post Deselect Post Link to Post Member Give Gift Back to Top Post by john8604 on Mar 4, 2016 0:07:11 GMT Thank you. This is inbred population. In other trait, lambda value of "mlma-loco" is near 1. Maybe I should use "mlma" for growth trait.

Post by john8604 on Mar 3, 2016 8:28:58 GMT

Post by Jian Yang on Mar 3, 2016 12:05:53 GMT

Post by john8604 on Mar 4, 2016 0:07:11 GMT