Hello,
I have a F1 progeny from two outbred parents (4way cross then) with no missing genotype information and with around 600 markers. R propose 4 methods for interval mapping (em, imp, haley-knott and extended haley-knott)
I wanted to know if I should do the QTL detection with the EM method proposed in R or if another method would fit better than this one for my case. I thought about the multiple imputation method but as I don't have missing genotype data so I am not sure I need it.
Furthermore, i would like to perform after that a QTL detection with Multiple QTL Mapping and i read that "multiple imputation (imp method) has greatest value for the fit and exploration of MQM models". So I am a little lost in the choice of the method for the first step of my qtl detection. Could you give any advice according your experience ?
Thanks
Dear Diana Carolina Lopez Arias
I proposed use Tassel software.
Tassel is a powerful tool to QTL analsis.
Thank you for your answer Mostafa Haghpanah but my question is not about the software but about the most interesting method to use in my case. I know that mapQTL uses the algorithm EM and I don't know, what does Tassel software uses as method ? Actually, I would like to understand the way that scientists choose their method so I can make a reasonable and thoughful decision for my analysis.
Dear Diana Carolina Lopez Arias
This paper could be helpful
https://www.jstatsoft.org/article/view/v040i07/v40i07.pdf&ved=0ahUKEwj8xuTA5rnYAhWGB5oKHX2eBZMQFgggMAA&usg=AOvVaw3z04qUhA9JejSsBfhiKjnh
Oh thank you for your help Mostafa Haghpanah ! I will read that then.
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