Phenotype data set up

[Bruno Saconi]

Hi all,

Might be somewhat of a naive question (I am new to QTL analysis), but I am wondering whether the phenotype data has to be set up as strain averages OR if I can use individual mice data. Based on the tutorial (https://kbroman.org/Teaching_CTC2019/CTC2019_tutorial.html), it looks like strain averages were used.

Looking forward to your insigths.

Thanks,

Bruno

[Karl Broman]

For the analysis of recombinant inbred lines, I prefer to focus on strain means, as for QTL mapping there's little additional information in the individual values, and the analysis is much faster and simpler.

You can do the analysis with the individual mouse data, but you need to take account of the relationships both in the analysis and particularly when doing a permutation test to establish statistical significance.

karl